What kind of accomplishment for a World Champion, who is meant to be the best in the world, is putting a non-wrestler without a string of muscle on his body 'out'? Who, by the way, has beaten him down with two others despite his lack of any physical ability. Therefore, they're booking Shane higher than their own World Champion (well, future World Champion since I'm going back before Backlash really)
Getting beat up is fine, if it's believable. Like I said, Vince was, because he was so god damn huge and he always gave himself a massive advantage. If it was Cena, Batista, even MVP, it would kind of make sense, even if it was a three-on-one situation, since that's what face wrestlers have been doing since the dawn of time. But to have the biggest heel on your show beaten down by somebody who's wrestled three matches in the last three years (all of which were hardcore spotfests) really makes them look weak.
I barely recall Shane being beaten down, all I really think of when I think 'McMahons vs Orton' is the initial attack by Shane with his fake punches, fighting most of them of week after week and his repeated ownage with a kendo stick.