After Faustus decides to study magic, these scholars get majorly worried. First they want to know his whereabouts. And when the find out that he has taken up with two famous magicians—Valdes and Cornelius—they freak.
Understandably, they're a bit worried about their buddy's soul. So they ask their teacher to have a word with Faustus, hoping a little education will persuade their friend to jump back to the Good Side.
That's the last we hear from the scholars until they appear at the end of the play, first requesting that Faustus conjure Helen of Troy (um, what happened to the whole magic-is-bad thing?), then counseling him to ask for God's forgiveness and praying for his soul as he waits for the devil to take it. It seems these guys are anti-devil, sure, but when the devil can help Faustus bring a beautiful lady around, well then they're more than willing to turn a blind eye to the Big Bad.
But for the most part, these guys are a force for good. The Scholars' role in the play is to show us the alternative path Faustus might have taken. Had he stuck to the study of the traditional academic disciplines and stayed away from magic, he, like these men, might have been assured of God's forgiveness and grace. Study hard and you'll go straight to heaven, they seem to say (remember that, Shmoopers).
Plus, the Scholars' attempt to save Faustus at the beginning of the play also increases Faustus's culpability for his fall. Even though his friends were totally trying to help him, Faustus ignored them, and persisted in his sins. So he has no one left to blame but himself.