It's complicated, but it basically had three things going against it:

1. The hype of the first two films, which were made with relative creative freedom.
2. Coppola hadn't made a big hit in several years, and it was becoming fashionable to hate on him.
3. The third film was made years after the first two, and Hollywood had changed. Seemingly the entire Hollywood machine was working against Coppola. He didn't get to make the story he wanted to make, he didn't have the time or the budget he needed, and Winona Ryder bailed at the last second, leaving Coppola to make a snap decision to cast his daughter, which was a mistake.

Personally, I also waited years to watch it because I heard bad things. And when I finally watched it... I thought it was actually pretty good. Not as great as the first film (still the best one, imho), but way better than people had given it credit for. The new edit of the movie, The Godfather Coda: The Death of Michael Corleone, was even better. I think it's a good ending to the saga, although it could have been better if Duvall hadn't asked for too much money, and Paramount had let Coppola make the movie he wanted to.