The main character, Kei, is not "cured" of her homosexuality like other reviewers are claiming -- that is never even portrayed as a desirable or healthy thing. Kei is definitely still a lesbian at the end.
Kei is a strong heroine, who has to deal with a mother who does not understand her, and so is sent to an all-boys school with the goal of getting her to like boys. The audience empathizes with her situation as she is forced to pretend to be a boy, deal with boys who scare her to the point of puking (but with comedy), and navigate the tricky situation of boys falling for her once they find out she is female.
Yet throughout the manga Kei stays true to herself, maintaining that she really likes girls. Near the very end she is about to act on these inclinations to transfer out to a school which does have girls. But it's very clear that she decides to stay for the friendships she has built. In the last chapter, when she's deciding whether to stay, she explicitly rejects staying for the reason of furthering a romantic relationship ("Because he said he likes me? No."). And when her would-be boyfriend asks for a reply to his feelings, she can only awkwardly turn him down. At an earlier time he even acknowledges that a relationship with Kei could probably never work out because she "likes girls." She's a lesbian, people!
The mangaka does a good job with the ending, making the school become co-ed -- no doubt to Kei's delight -- and thus allowing the possibility for healthy same-sex relationships for Kei in the future.
What threw so many of the reviewers off was the very last scene where Kei lightly takes the hand of the would-be boyfriend. It's a sweet ending, and the small action was well within Kei's character given the situation.
But to interpret these last 3 pages as somehow reversing all the development and repeated confirmation that Kei likes girls throughout the entire manga is ludicrous! You have to be either stupid or looking for a reason to call this manga homophobic, or both, to believe in this magic, 180 degree character change. Give the mangaka a little credit, yeesh!
This manga is really the opposite of homophobic, since the reader gets to struggle alongside the lesbian MC and understand some of the challenges of growing up not-straight, including what an uncooperative parent can do to make your life difficult.
Houou Gakuen Misoragumi is fresh and funny, less focused on romance than most shoujo manga, and more mature. Definitely recommended.