Yes, but does that mean anything if they don't profit at all from it? Ratings mattered as a comparison when Nitro was on the air, and they don't really matter at all now because they don't mean anything, except that USA can charge "x" number of dollars for ad revenue. House show attendance spiking after Edge won the title and the Rumble PPV buyrate being higher than it was last year would show an interest from the fanbase in spending money to see Edge defend the belt. As it stands, there's no proof of such a thing.
As far as ignoring the crowd reaction, there was no reason they couldn't acknowledge it on the air, of course, but unless Cena was actively turning fans away from the product, there was no reason to take the belt off of him. It was a reaction. If anything, the fans were reacting like they wanted instead of like WWE told them to, but it wasn't adversely affecting anything at all. I think the booing of Cena was like the "What?" chant in many ways; people saw it happening on TV and it caught on in the arenas, but eventually, fans would tire themselves out on it. It has little to do with actually hating Cena, and even if it did, unless he was pushing people away from the product, it's still a reaction and it doesn't really matter at all.
HHH is right that Cena has also been paired with guys who have no idea how to get heel heat. Not that HHH will do it any better or anything, but his point is correct.