It wasn't his methods. His idea of curing by talking is now standard practice, but was revolutionary for that time. The problem was that it put him on the path to exposing the widespread incest and rape that was going on in his society. Freud initially believed his patients, but wasn't prepared to face the consequences, so he changed his tune, and this reversal led him to come up with the far-out psychosexual theories he's so famous for.

Freud is still regarded as the father of modern psychology, perhaps because he was the first to actually sit down with his patients and take them seriously.

Here's an article that tells the story in detail: http://www.theatlantic.com/magazine/archive/1984/02/freud-an...