Largely because for many of those very fans who began booing Cena, Batista was the "wronged" party. They were backing him and anointing him over on Raw, but by the summertime Vince and the company at large was illustrating that it would be Cena, not Batista, who would be positioned as the true #1 man in the company by having Cena traded to Raw. The resentment towards Cena was at its core about how Vince and WWE were pushing him as their new Hulk Hogan, Face of the Franchise, and in doing that it was Batista who was made #2.
I also think that Batista's main event angle that saw him reach the top was more organic in every way: the fans chose him, he finally turned on Triple H, and the whole thing just snowballed. Vince and the writers had to catch up with the fans, in a way that wasn't dissimilar from Steve Austin and Bret Hart being double-turned at Wrestlemania XIII. Batista was still enormously hot from that angle (which was just concluding then) in mid-2005 when Cena was traded to Raw.
That isn't taking anything away from Cena or his rise. He was, actually, more over than Batista a full year or more before Batista's ascension began. However, from the time period of around October 2004-October 2005, the fans were still rabidly into Batista, and Cena, while huge in his own right, was receiving a push whose moving parts you could actually see. Batista's virginal main event storyline was kind of magical.
Pretty much this.
The fans chose Big Dave in 2004 and his push was, as stated by DR, organic. It felt natural and it was welcomed by the fans. It's why they remained behind him in a such a strong way. Cena's push felt very manufactured in comparison to his (in 2005), and I think the trade of Batista to Smackdown kind of made the Raw fans rebel because he wasn't the one they chose and it became obvious very quick what WWE was trying to do.
One has to remember Batista was pushed much stronger than Cena in 2005 and didn't receive a backlash. He steamrolled Chris Jericho, Benoit, Triple H, JBL and Eddie throughout his rise. He also was manhandling Big Show/Kane/Shawn in the SVR feud and essentialy dominating all the time.
In ring skills: Cena and HBK had awesome matches. Cena pulled out a good match from Khali. Batista and HBK had one of the most boring matches I've ever seen on Raw. I can't think of any good Batista matches.
I agree Cena is better in the ring than Cena but I can't fathom people who state they can't remember any good Batista matches.
He had one of the greatest Hell In A Cell matches of all time with Triple H, a good match with Eddie at No Mercy 05, a good match with JBL at Summerslam 05, he had around five great matches with Undertaker, he gave Khali his second best match in the Punjabi Prison, he had two (three if you want to count their match back in 03 I think) good PPV bouts with Shawn (I find it weird how you do not know of these yet know of their boring Lumberjack match from Raw), two great matches with Jericho, great matches with Edge, MVP and he's the only superstar who gave Kane a great match in a normal bout aside from Benoit in the last 6 years.
He may not be Eddie in the ring, but Batista has had more than his fair share of good/great matches.
Mic skills: Cena all the way. No contest.
Definitely.
Company man: Cena all the way again. He gets exposure in outside media, which kind of goes back to the talking thing. Batista is not good on the mic even outside of wrestling.
I also agree there. But I think you're downplaying Batista's significance here. He was WWE's biggest international superstar between 2005 - 2008. And he's done a lot of promoting for them in general, especially overseas.
Merchandising: I don't even know if I'd ever seen anyone wear a Batista shirt. Cena wins here too.
Cena kills everyone in merchandise.
General human being: Cena does Make-A-Wish and seems like a genuinely good person. Batista cheated on his wife, who had cancer, with Miss Botchamania Melina and threatened a 14 year old (I may be off by a year or two) with a pool cue.
You should probably know these were lies made up by the dirtsheets.