I thought you might like a female perspective.
I think what concerns me the most is you were fighting a lot before the cheating, so something was already wrong before she strayed. Please don't interpret that as me saying you share in the blame of her cheating, not even remotely implying that. She was wrong, and reacted to a bad few weeks in her relationship in an immature and impulsive way. Is she like that in the other areas of her life? Your continued fighting is also something to consider when deciding whether to end this relationship.
The cheating sounded physical more than emotional, and sometimes the latter can be harder to forgive. She confessed it, so she definitely felt bad about it. If you had found out on your own or through a third party, that would have been worse. Who was this guy? Random guy in a bar, co-worker, old friend? Any chance of further contact with him? That is something to consider. And how hard is she working to re-earn your trust? She can't do that by just apologizing continually. She should be an open book and willing to answer any questions you have, whether it be about the affair, her emails, whereabouts, or phone calls.
Cheating can take a long time to get over, so don't expect this hurt to go away anytime soon. Sounds like the two of you were together during college, and a long shared history is a hard thing to let go. I advise you to put some space between the two of you again, or at least don't just go back living together and just stew about this silently in your own mind. "Working it out" is not moving back in and hoping the hurt goes away over time. You need to really think hard about what you want. Forgiveness is a process and a conscience decision, and one you have to work at, sometimes everyday. If you find you just cannot forgive her, and she's not working hard to earn your trust, you have to let this relationship go. All you'll do is punish the both of you, and that is no way to live.