It's an interesting move for sure, but it should be taken as no more than a personal choice. Nobody should really be offended since it doesn't affect you personally.
If you want my opinion, I'm with Pokoko and Ka-Pi in that the decision to make Link male in the game was the decision of the creator, and thus there is nothing wrong with experiencing the work of fiction for what it is. Besides, a lot of "male" protagonists and characters in Japanese media are androgynous and may be biologically male but dress or look on the more feminine side (yo Tidus, women cosplay you the best just sayin'). Thus, someone whom is transsexual may see heroes like that dressing or appearing feminine and identify with them in that regard.
For any other reason there are RPGs. You can do whatever the hell you want with your character in RPGs.
#1 Amb-ass-ador
