Well in view, the thing about that time was about anarchy, people use to embrase the anti-heros like never before, the good guys that were supposed to be loved started to be hated and booed, first exmaple before the Rock was Shawn Michels at 1996 Survivor Series (Actually the night Rocky debuted) when he faced Psycho Sid, I mean Sid was a tweener at the time and Michaels was the biggest babyface at the time and people turned on him that night, eventhough Sid won in a clear heel fashion, That nig Bret also face Stone Cold for the very first time and eventhough Austin got booed, that night people really started embracing Austin and turning on Bret.
Rocky defeated HHH on a Thursday special fo Raw to capture his first Intercontinental championship just about 4 months from his debut, but the character was bland and even The Rock recognized that sometimes it was too goo and the strangest thing was the He had to keep smilling even when it was supposed to be down.
By the time the competition with WCW was very stiff and well, people were getting tired of the "good" guys, the only one that didn't have much a problem was The Undertaker but he has never being a complete true face in his whole career.
John Cena and The Rock can be compared but only at the beginning of their careers, befoe Cena became a rapper, because once The Rock was unleashed, the character was always remaing on the same tone, with some little changes from heel to face and face to heel but the escense remained the Same, Cena on the other hand passed from the rapper to the "marine" type of guy and it is a change that has been significant, while the Rock was becomming edgier and edgier (also because of the era he was in), Cen has toned downn a lot (also to be the representative for this era) to mark way better between good and bad guys.
About the signs, it is way more controlled now and that also helps WWE to push who they want and to control what gets on TV, while they do not control what the crowd does or try to, with editing for taped shows it helps get things done.
In 2006 when RVD won the title, they knew that was coming and never tried to control people of the old EC arena, actually embraced the idea so Cena could be "against the Word" and therefore, justifying the lost to RVD, even people thanked Edge for the interference.
Just something out the sign stuff, There was reference to the "If Cena Wins, we riot" sign, well on Summerslam of that same year Edge faced Cena for the title in Cena's Hometown, and some guys had pretty much the same sign but with the opposite message, I thing it said "If Cena loses, we riot", it was so funny and sad at the same time when Edge retained and actually got cheered by the crowd, these poor guys had to take away their sign and were almost crying, I am not a Cena Hater but I am a fan of Edge's work so for me that was damn funny.