I think the problem lies in a simple comparison. We know that in the past, main eventers have been able to speak their mind to the authoritative figures and felt confident as if they have free reign to do so. It wasn't even just a "balsy" thing to do, it was more like an unsaid statement of "You may run the company but I AM the company!" type of thing. Stone Cold, Triple H, The Rock and even Chris Jericho had that attitude. And today, John Cena and Randy Orton share that attitude. Albeit they're at opposite ends of the morality spectrum with their intent when stating it but nevertheless, they have that attitude. This is a good thing but there's one thing noticeably different.
The men I mentioned first, were mouthing off at an authoritative figure in Vince McMahon who was not a muscle-bound 40-something Triple H - who visually rivals both current main event champions. Not to mention, this guy has lots of accolades and built-in crowd respect. Back when Vince was being treated like crap or delivering scathing speeches, he often had protection in DX, The Rock etc. This provided him his often unwise swagger that gave him the "testicular fortitude" to say whatever he wanted. But even with this advantage, he OFTEN had moments of weakness where he'd be threatened, turn tail and run after being on the losing end of a stare-down, or be backed into a corner. Triple H CANNOT be an authoritative figure that cowers from a guy smaller than him. After HHH's take-on-the-world persona for over a decade, it would look too ridiculous and unbelievable to a crowd who has more recently seen him take on Undertaker and Brock Lesnar without fear. Knowing HHH's character is supposedly this powerful, is what's hampering Orton's ability to get a response from the crowd. When Orton yells at Triple H, you get the sense that Orton's about to get his ass kicked. I'd say at this point, the only wrestler who has been built-up through kayfabe to take on such a power as HHH, is Cena. This is the flaw of having a (very over) main eventer as "The Authority". His presence overshadows everything that a typical main event champion does.