It often looks to us like medieval Europeans were confused about what Islam "actually was." A handful of scholars in the west did make an attempt to understand it for the purpose of countering its arguments to demonstrate why Christianity was superior. However, what we see especially in more popular texts like Roland is a range of different portrayals that...well, don't really resemble Islam. Some of this was because they didn't know, some of it was because they didn't care enough to know, and some of it was because there were conventions of what made someone "evil" or "bad", and if Muslims were evil and wrong, then Muslims surely fit into those conventions.

With Roland's "unholy trinity" of Mahomet, Apollo, and Termagant, two things are at work. First, the poem portrays Islam as the anti-Christianity. If Christianity has a Trinity that is its one God, Islam has a reverse trinity that is its false gods.

Second, the choice of Apollo is a deliberate reference to--as you point out--Greco-Roman paganism. In the medieval Christian mindset, that meant worshiping idols of rock and gold. The idea here is to portray Muslims as idolators. You could see a vague reference to the Kabaa, which medieval Christian polemic portrays Muslims as worshipping, or that could just be a 'deep background' that the Roland poet wasn't directly aware of, but influenced the stories he had heard about Muslims.

The choice of specifically Greco-Roman gods was a long-burning development in medieval literature. It tied Muslims to the pagan Romans that Christianity had defeated, carrying the promise that Christians would defeat this new threat, too.