Why does Holden spend so much time with Ackley if he can't stand him?

Holden is a very lonely boy. He feels especially lonely now that he has been expelled from Pencey and does not belong there even though he is still living there. He is an outsider, a non-person. He has also been "ostracized" by the fencing team because he lost all their equipment on the subway. He spends a lot of time talking to Ackley because he feels lonely and has no one else to talk to. After he has a falling out with his roommate Stradlater, he doesn't want to stay in their room. Although Holden doesn't say so, Ackley is another lonely boy. They have a lot in common. Ackley is a loner because he is homely, has a disagreeable personality, is not athletic, and for other reasons which become apparent in his interactions with Holden. 

It may be inaccurate to say that Holden can't stand Ackley. He may be annoyed by some of Ackley's actions and attitudes, but at least Ackley is someone to talk to. The reader can sense that both these boys are putting on acts, hiding their real feelings, which are unhappy ones. There are always insiders and outsiders in schools, offices, and everywhere else, and Holden and Ackley are both outsiders. Holden is an outsider because he is a nonconformist. Ackley is a conformist but is an outsider because of his unfortunate personality. The name Ackley suggests that he is a homely guy with bad teeth and a bad complexion. A geek. He has a big inferiority complex for which he overcompensates by assuming an "attitude." His cynical, superior attitude only helps to alienate him from other people. He might be compared with the character Crooks in John Steinbeck's Of Mice and Men. Crooks is ostracized by the white farm workers because of their racial prejudice. In reaction, Crooks has developed an attitude of contempt, superiority, and preference for solitary introspection. We know that both Crooks and Ackley would love to be accepted.

In his famous novel Lolita, Vladimir says that Lolita's friend Mona Dahl is "burdened" with an IQ of 150 (which is Near Genius). Why should such a high IQ be a "burden"? Holden obviously has a high IQ, although he thinks he is "dumb" because he has flunked out of three schools. But his near-genius IQ makes him a sort of freak among boys of average intelligence. They sense that he is smarter than they are, and this doesn't make them like him. In Shakespeare's As You Like It, Adam, the old family servant, tells Orlando, quite accurately, that superior gifts can bring their possessor hatred and envy rather than admiration.

Know you not, master, to some kind of men
Their graces serve them but as enemies?
No more do yours; your virtues, gentle master,
Are sanctified and holy traitors to you.
O, what a world is this, when what is comely
Envenoms him that bears it!
                     As You Like It, Act 2, Scene 3

It is significant that when Holden is leaving Pencey to go to New York: 

When I was all set to go, when I had my bags packed and all, I stood for a while next to the stairs and took a last look down the goddam corridor. I was sort of crying. I don't know why. I put my red hunting hat on, and turned the peak around to the back, the way I liked it, and then I yelled at the top of my goddam voice, "Sleep tight, ya morons!"

Holden would like to stay here. He would like to be one of these boys. But he can't. He doesn't know why he is sort of crying--but we do!