Eyes certainly are a dominant recurring motif in A Midsummer Night's Dream. We can even find many references to eyes in the first scene alone. There are a few things that eyes symbolize; two of those are perception and understanding.
We first see how eyes represent both perception and understanding when Egeus petitions Duke Theseus for the full force of the law should Hermia continue to refuse to marry Demetrius. When Theseus argues to Hermia that "Demetrius is a worth gentleman" and that, even though Lysander is also worthy, Hermia must consent to her father's choice, Hermia's reply is "I would my father look'd but with my eyes" (I.i.53-58). In other words, Hermia is stating she wishes her father could see things the way she sees them, that he had both a broader perception and understanding of Lysander's merits, showing us how eyes represent both perception and understanding.
A central point of Shakespeare's is to show just how arbitrary the feeling of love is. Egeus has no real reason to prefer Demetrius over Lysander, nor does Demetrius have any real reason to prefer Hermia over Helena. Helena also shows later how eyes represent not only perception and understanding, or rather lack of, but also arbitrariness later in her own speech. Helena points out that she is just as beautiful as Hermia, and that "[l]ove looks not with the eyes, but with the mind," meaning that love is really based more on figments of the mind, figments of the imagination, rather than on anything real of concrete (239). She further states that due to the arbitrariness of love "wing'd Cupid is painted blind," showing us just how much eyes represent lack of perception, understanding, and also represent arbitrariness, particularly the arbitrariness of love (240).