The answer to this can be found in Act II, Scene 2.  The short answer is that Caliban thinks Stephano is a god because Stephano gives Caliban some liquor.

This happens when Stephano is walking around, drinking (he's pretty drunk already).  He sees Caliban and goes over to talk to him.  He can't really figure out what Caliban is, but he still thinks that the thing to do is to give Caliban some of the liquor that he is drinking.  Caliban has apparently never drunk liquor before and he thinks that it must be something that would come from the gods.

Here's a quote to show this:

That’s a brave god and bears celestial liquor. I will kneel to him.