This is not necessarily true for non web apps. I love Cocoa for instance and the MVC pattern is great for most kinds of apps. But not for the web, IMHO. It's overkill.
There are too many unnecessary abstractions from the protocols. The LAMP stack already gives you everything you need. For instance, PHP with mod_php already is a template processor. There's no need to build another one on top of it. Unless you don't know what you're doing, which is bad anyway.
I still prefer to parse the query string myself, to define my SQL queries (and most of the times a single query can replace 4-5 queries generated from a framework so apps are much faster) and to keep the data as clean and separated from the code as I can (data is always much more important than code and it's much better if it is code agnostic).
With web frameworks there's a lot of magic and it's faster to have a web app up and running. But it's a pain as soon as you want to modify the default behaviors. At least in my experience.