It's hard to say what disappointed or confused fans the most about The Phantom Menace, but you could claim that the first thing to really trigger a wave of negativity was the title. From what I can tell, internet polls at the time showed that roughly 25% of people didn't entirely hate it! Fans had been hoping for something that sounded epic and cool, something like Balance of the Force, or Guardians of the Force, or Children of the Force ('the Force' seemed to show up a lot in rumoured titles).
By comparison, The Phantom Menace sounded cheesy, childish, hokey, and old-fashioned. Some people loved it because it sounded like a chapter in a Flash Gordon or Buck Rogers serial from the 30s, others hated it for the same reason. Some were even convinced that a title that bad had to be a hoax, maybe caused by someone hacking the Star Wars website, maybe planted by George Lucas himself as part of a cunning deception!
Personally, I have no idea what I thought of the name when I first saw it. At this point, it's just the title of the film for me and I wouldn't want it to be called anything else. And I have a feeling most of the people who hated the name eventually accepted it and moved on... to complaining about Episode II being called Attack of the Clones.
SPOILER WARNING: I'm going to write about the ending of the film and then share my thoughts about the movie overall. I'll also be spoiling things about the Original Trilogy films, but nothing about the Sequel Trilogy, the cartoons or the TV series. I won't spoil anything about the Ewoks movies either, but that's just because I don't actually know anything about the Ewoks movies.