So, it's time for a theory! *intro music*
Here's the theory...
Do you remember that memorable scene in The Incredibles in which Edna Mode says that famous line?
In the scene, she lists a bunch of superheroes that have been killed simply because they wore capes, such as Thunderhead, DynaGuy, and Stratogale.
Now, Edna is known for designing supersuits for many superheroes. Everyone comes to her because she is the "best of the best". So, it's likely that all those superheroes came to her for supersuits. She gave them capes, and this likely means she believes she's responsible for the death of the supers.
She didn't give Mr. Incredible a cape because she knew he was a good hero.
And if all supers came to Edna for a suit and Syndrome wanted to be a super, he probably wanted Edna to make him a suit. Edna likely knew that Syndrome was evil and/or not really super, so what did she do?
She gave him a cape.
And eventually, his cape is what killed him.