It's impossible to point at a single thing and say this is why a movie bombed. In Clue's case, it was multiple things.
To be fair, when Clue opened in theaters on Dec. 13, 1985, it was an unambiguous flop, ultimately grossing just $14.6 million (or $31.8 million adjusted for inflation). It was also massacred by most critics, many of whom were dismayed by the then unprecedented — and, for the time, scandalously crass — notion of basing a feature film on a popular family board game. “Fun, I must say, is in short supply,” sniffed Roger Ebert in the Chicago Sun-Times, while Janet Maslin of The New York Times bemoaned, “there is so little genuine wit to be found in Clue.” Not helping matters: those multiple endings. While they play back-to-back now on cable and home video, they were separated out for the movie’s theatrical run — one theater had ending “A,” another ending “B,” and so forth — a marketing gimmick that became the most common target of critics’ scorn.
First, it was panned by professional critics, before the time of crowd-sourced reviews on the internet. Like most "cult" hits, most people think its so bad its bad, not so bad its good. From wiki:
The film was initially received with mixed reviews. Janet Maslin of The New York Times wrote negatively of the film and stated that the beginning "is the only part of the film that is remotely engaging. After that, it begins to drag." Similarly, Roger Ebert gave the film a 2 out of 4 stars review, writing that despite a "promising" cast, the film's "screenplay is so very, very thin that [the actors] spend most of their time looking frustrated, as if they'd just been cut off right before they were about to say something interesting."
The film holds a 62% positive rating on the film-critics aggregator website Rotten Tomatoes, with an average score of 5.8 out of 10.
Second, the movie was based on a board game. This is way before the time of mega block buster game or toy or cartoon adaptations that make too much money for the crap that gets passed as a film (i.e. Transformers and Battleship and Gem and anything to do with Hasbro really).
Third, yes, the multiple endings. Not being able to see "the" true ending probably had something to do with it. Who wants to pay 30 dollars, drive to multiple theaters, spend 6 hours with 5 being repeated scenes, to see the whole picture when the competing movie does it in 10, a single theater and 2 hours. (Or how ever much a movie ticket cost in 1985).
Tim Curry himself puts it best, regarding why most people don't/didn't like it:
“I think it’s a lot of fun, you know?” says Curry. “There are some very funny people in it. Why else? I don’t know. It’s not something you can really judge, I don’t think. Because in some ways, a film either works or it doesn’t, and sometimes it works after it seems to have not worked. … I think it’s a question of people’s sense of humor.”