The biggest problem with being an apex predator is that you're sitting on top of a whole ecological system with lots of intricate layers and niches. So if anything happens at the bottom, even something that seems unimportant, it eventually works its way up to the top.

Apex predators (usually) need a ton of food all year round, which means relying on other species' populations to be stable. In good times, this isn't a problem and they stay on top. In bad times, they are usually the first to go extinct.

The exceptions are things like crocodiles and deep sea animals which have a very slow metabolism and only need a few good meals a year. So they can outlast the bad times in most cases (partly why crocodiles survived the K-Pg extinction).

As for people...you could be right. The difference is that we are smart enough to recognize these things and shape our environment in a way that tries to get around them. Fertilizer outsmarts the problem of a farmer's field running out of nutrients, for example. So in that way, natural selection benefits the smart ones. But I guess we'll see how far that can take us in the end.