I've always had two things against code generators. The first is like Mark said - they're great for new code, but if you make any changes you're SOL. You either lose the use of the generator (for that file at least) or you lose your changes.
The second problem is likely outdated, and not quite code generator specific, but it's close enough that I always think of it when I hear about code generation. Many moons ago, when I was a fledgling young web developer, I came across Microsoft's FrontPage. I thought it was awesome at first - draw your webpage? Great! Then I saw the generated code. Absolutely horrid. Even as a total HTML noob I knew that was awful code. Always cringe a little when I think of an algorithm creating code.