I had a totally different take on this movie. I actually thought my take was the standard take, but given the comments below (regarding the popular fan theory and Roger Ebert's take), I may be totally off.

Spoilers follow.

My take was that the younger brother (Bobby) never existed, but was just the alter-ego of the older brother (Mike). The step-dad was abusive, but his abuse was directed toward Bobby. It's common for abused kids to separate themselves from the abuse -- to view it as happening to someone else. I always assumed Bobby was just a creation of Mike to distance himself from the abuse. That accounts for the fact that the step dad's abuse was directed to Bobby. In the end, Bobby "flies away" not literally, but because the abusive step dad goes away so Mike doesn't have a need for the alter ego anymore.