Okay, here is my condensed reaction to why I would boo Damon: he went back on his word.
Yes, baseball is a business. However, if you work for Sun and bolt to work for Microsoft, your former coworkers won't exactly be cheering for you as you return to Sun after sharing all of Sun's secrets with Microsoft. There. "Baseball as a business" argument discarded.
Furthermore, if you are going to do something for yourself, say you are going to do it for yourself. At one point, Damon was quoted as saying that the extra money he earns with New York could "help a lot of people." Yeah, him and his wife. (Sorry, too much to do or else I would dig for the quote).
Lastly, and most importantly: he broke his word. On May 25 of last year, Damon said that he might leave the Red Sox, but would never play for the Yankees. I do not like liars.
Yes, Damon helped us win the World Series. For that I am grateful. However, think about Ford's CEO bolting for Dodge. Would you as a Ford employee still love him for something he did years ago?
It's like a man cheating on his wife and her saying, "Well, he cheated on me. But we went out for a really good dinner two years ago." Nuh-uh. Ain't gonna happen.