Well, I'm still trying to find the answer to that as well. But I found on several websites that it was named after Richard Boyle, 3rd Earl of Burlington, England. He was a prominant aristocrat and well known architect of the time when the land was granted. I will note though, that I am biased as I my name is Richard Boyle.
The second school of thought regarding the name origin is a prominent New York family named Burling who owned large tracts of Vermont land but are not listed as grantees in Burlington itself. Some of their land grants however were issued on the same day that Burlington was established.