Firstly, Caliban joins forces with Stephano and Trinculo because this subplot serves as a comic relief for some of the more serious scenes in the play. Caliban's first exposure to alcohol, Stephano serving as a 'ruler' and Trinculo's witty remarks all contribute to the comedic exploits that take place later. Remember, that the play is a comedy and needs light-hearted subplot.
Secondly, Caliban sets himself up as a character who needs to be ruled. Even though he is native to the island, he values Stephano as a leader. This is important concept because in the mindset of an Elizabethan audience they felt justified in overthrowing and governing New World peoples. His submissive behaviour and willingness to serve white rulers therefore justifies England's actions in the New World. If there was resistance from Caliban, the morality of Prospero's rule would be called into question.