Ever since the announcement of a new Star Trek series set for release in January 2017 with a pilot on CBS followed by the series being uploaded to CBS All Access, CBS' streaming service competing with Netflix and Amazon Prime, likely in the hopes of being the service's killer app. Ever since the announcement, however, there have been fears that the series would be set in its own universe, or worst, set in the "Abramsverse" as the twin reboot movies are colloquially known. These fears are justified, though I would say ones that fans everywhere shouldn't worry about. Though it is possible that it will be the case, I believe otherwise for three reasons.
1. CBS has full control of the Trek franchise on the small screen
Something that many people, fan or otherwise, is unaware of is the fact that Star Trek is not wholly owned by Paramount. Though this used to be the case, in 1994 Viacom purchased Paramount, placing both companies under one roof (Viacom originally started as a rebranding of CBS) and it was decided that Paramount would be responsible for the Star Trek IP for the big screen while CBS would be responsible for the small screen. This deal initially worked out for the better, with 1995 seeing the launch of United Paramount Network, or UPN, in an attempt to create a fifth national over-the-air broadcast channel (launching the same year as Warner Brother's "The WB") which saw Star Trek: Voyager premier on its first day of broadcasting as its flagship series. What followed was a decade of troubled production for a network that never managed to find a killer app for its network, the age of cable and syndication creating competition the network simply could not manage to meet, and in 2005 was shut down for good (the remnants where merged with that of The WB, which was shut down in 2006 and turned into what is today The CW, jointly owned by CBS and Warner Brothers). How the Trek IP landed squarely in CBS' hands, however, came about in 2006 when Viacom elected to split the movie production and distribution parts of the company from the television broadcasting part of it, creating CBS as an independent corporation and a new Viacom which held Paramount as the backbone of its corporation. When this was done, the Star Trek IP was not put into one house but instead retained its status as having the movies be under Paramount's control, while the television series was under CBS' control. With the bulk of the prime universe being television series, specifically 5 series spanning 28 seasons, they have an intensive to have these works remain in the public eye, and in the age of binge watching there's no easier way of doing that then having an ongoing series which can be tied back in with the older series. But that isn't their only incentive.
One may think it is an obvious statement, but merchandise is a major part of the entertainment industry. Whether it's because it's the only way to turn an industry-wide profit (such as with Japan's Anime industry), being the main source of revenue (Lucasfilms before the Disney buyout, which was making 80% of its revenue from toys), or simply a means of making more icing on the cake (most cable series) merchandising is big in the entertainment industry, and Star Trek is no exception. Whether or not you've bought them, we've all seen toy action figures of the cast from at least one series or another (typically the original or Next Generation), toy phasers, maybe a cheap communicator, and for those of us who frequent comic book stores Star Trek Tactics, a game based on Heroclix using ships from the series. With how much of an influence merchandise is on the entertainment industry, with whole movies or series existing only to sell toys, there's no doubt that there will be a long list of new items on little Timmy's Christmas list, because you showed little Timmy Star Trek at an impressionable age instead of Star Wars. And something to keep in mind is that even at the hight of the marketing blitz for Star Trek '09 and Into Darkness, the lion's share of merchandise being sold was for the Prime universe, particularly the Original Series and Next Generation. It seems that the market wants more Prime Trek merchandise, and CBS would likely want to capitalize on that, though there's always revenge as well, which brings me to my last point.
3. CBS is not on good terms with J.J. Abrams
J.J. Abrams is many things to many people. Most people know him for one of three things: Mission Impossible III, Lost, or Star Trek '09. Opinions differ for fans and critics about whether he's a genius or a hack, and the corporate world is no different, with the full range from Disney's love of his ability to make a series with an outlandish premise become a massive hit, to CBS, who loath the man for his business ideas he pushed that where, in kind words, less then pragmatic. To make a long and boring story short, Abrams had great ambitions for the Star Trek reboot movies (despite openly being unfamiliar with the source material and not a fan, which itself led to problems that ironically are mirrored with Star Wars for the opposite reasons, that property being one he's too much of a fanboy of by some accounts). Abrams wanted the movies to be more then just movies, he wanted them to be the basis for a new multi-media franchise that would use them as their backbone, with new television series, games, books and the like being made (with his company Bad Robot being the ones producing them for distribution, of course).
Now this doesn't seem bad on the surface, at least from a business stand point, but Abrams took things one step further. He didn't just want to create a new Star Trek, he wanted to create THE Star Trek. His grand vision was to have the universe we all call the "Abramsverse" supplant the Prime universe in every way, with hopes that some day the only thing you'd see on television reruns was series made by his company, and the merchandise being of those series and movies that he'd have a hand in making through his movie and television production company (and, by extension, royalties for licences materials said company created). CBS was not a fan of the idea for two reasons, first being the fact that the aforementioned merchandise has always, even at the high point in marketing for the new movies, sold far better for Prime universe items, and the second is that by having Bad Robot create the series (and by extension the new merchandise for it) the lucrative loyalties would go to Bad Robot instead of CBS, at least in part, but a large part of a very large pie. Abrams has always been notoriously hard to work with from the business side of things (Lost, for example, had him straight up lie to ABC about what the product was going to be, so it was only through its massive popularity that he still has a job, as he'd likely have been blacklisted from the industry had it failed. Whether this would have been a good thing depends on who you ask) and this attempt to completely rake over an IP he openly did not care about left Bad Robot and CBS on bad terms. For this reason we may see the new Trek series set in the Prime universe alone, as spite has always been a large part of the entertainment industry.
I won't discount the possibility that the new series will be set in its own universe or the "Abramsverse", however as it stands I'd say the Prime universe is the Prime candidate for the setting from a business perspective. This isn't even touching upon the writers and producers likely wanting the same for reasons such as the ease of working with pre-established settings compared to creating new ones, of the fact there's a large pool of actors from the previous series who could be called upon to become guest stars or even regulars who have minor fan bases of their own, but that's an article for another day.