Except we don't actually know what happened to those alternate universes, because we as the audience are only seeing the perspective of the 'prime' universe. Let's take "Yesterday's Enterprise" as an example. Due to the actions of the Enterprise-C being thrown into the future, it created an alternate future timeline where the Federation was at war with the Klingons. By returning to the past, the timeline "righted" itself. But how do we know that the other war timeline didn't keep existing, and we just don't see it? The Abrams films made it clear that the Kelvin universe is an alternate one, branched off from the 'prime' timeline when Nero was thrown into the past. But the 'prime' universe still exists; only in this case we the audience are now seeing the Kelvin universe instead of the 'prime' universe. One of the Star Trek novel writers even used this premise in one of their books, a sequel of sorts to "City on the Edge of Forever." In that book, the alternate timeline created when McCoy went back to the past and kept Edith Keller from dying (before Kirk & Spock "righted" the timeline) still existed, where McCoy was never rescued by Kirk & Spock and that timeline ended up with Germany winning WWII like what Spock saw in the future news reports.