I think a little too much emphasis has been made on the fact that this is supposed to be a "gay film", especially when the film was shown abroad.
But it's mostly a film about romantic love, adolescence and being different (Agnes) or wanting to be different (Elin).
It's not a film about homosexuality per se. The same story with two boys would have been unthinkable. It wouldn't have been as romantic and not at all as easy to accept by the audience. It would have been a different film altogether.
There is hardly any sexual matters in Fucking Åmål, only a little kissing and a very brief scene with Rebecka lying on the bed, fully dressed, caressing herself.
A few more scenes of tender intimacy with Agnes and Elin I'm sure no one would have had anything against.
But it was a sensitive subject since the girls were so young, and again, showing this wasn't the main point of the film.