You also have to consider the guy that comes out looking the strongest usually gets cheered anyway. That explains a lot about Austin (Stone Cold? Look weak? Never.), Rock (The guy is basically what Hogan was back in his prime, just a better worker), and HHH (Never loses, never looks weak, gets plenty of airtime).
Eddy is a guy who was just a face a few weeks ago, and was turned face by the fans in the first place. He's one of those guys it's just hard to boo. (Except when he's REALLY trying to be a heel. Example: Eddy v Rey at Haloween Havoc '97)