Theseus's disbelief in the fairies symbolizes the distinction between the world of the imagination and the world of rational reality.
As critic George Bonnard points out, in A Midsummer Night's Dream, the fantasy world and the world of reality never actually meet. Theseus represents the rational world, and his disbelief in fairies also symbolizes the rational world.
Theseus is the ruler of Athens, and as the ruler, he must always make use of his rational judgement. We see him employing his rational judgement in the very first scene when Egeus petitions Theseus for permission to enact the "ancient privilege of Athens," referring to the lawful right for a father to either kill his disobedient daughter or to send her to a convent (I.i.42). Theseus uses his rational judgement to agree that the law should be employed if Hermia continues to disobey. As a ruler, he knows how important lawfulness is in maintaining a society. Hence, as a ruler, he would not empathize with Hermia's opinion, even if he believed that she is right and Egeus is wrong.
We further see Theseus placing more value on the rational mind than the imagination when we see him proclaim that the Athenian lovers' stories of their night in the woods are pure fantasy and that imagination belongs to the lovers, the poets, and the madmen (V.i.8). Also, Theseus encourages the mechanicals' play to be performed, even though he is told that the mechanicals have no skill, because he feels it is his duty as their ruler, especially because the mechanicals have put the play together in order to pay Theseus homage. In return for the homage the mechanicals want to show Theseus, Theseus wants to pay them respect in return, as we see in his lines:
I will hear that play;
For never anything can be amiss
When simpleness and duty tender it. (V.i.87-89)
Since Theseus is viewing the play out of respect rather than because he is fond of an imaginative performance, we see once again that Theseus embodies the rational side of the mind rather than the imaginative side. Hence, since Theseus represents rationality rather than fantasy, we can say that Theseus's disbelief in fairies also symbolizes rationality rather than fantasy.