I wouldn't say it has a bad rep so much as it has a mixed rep. If your project follows the "convention over configuration" paradigm advocated by Maven then you can get a lot leverage out of it. If your project doesn't fit well into Maven's world view then it can become a burden.
To that end, if you have control over the project, then Maven may be the way to go. But if you don't and the layout is determined by someone not a fan of Maven, it may be more trouble than it's worth. The happiest Maven projects are probably the ones that started as Maven projects.
