... you all know that Winnie the Pooh was traditionally animated, right? It was even released the same day as Harry Potter and the Deathly Hallows: Part II, and still did well at the box office.
The Princess and the Frog wasn't a financial failure by any means, it's actually one of the few traditionally animated films that's done well and was universally praised in the 00's (some people even said it was their best film since The Lion King). The only reason Disney thinks it could have done better was because of the seemingly girl-oriented name, hence why they gave such gender-neutral names to Tangled and Frozen, and more than likely why Pixar opted to name their newest film Brave.
It really isn't because the medium has gone down in popularity, it's because most of Disney's films released after Tarzan were... well, to put it bluntly, pretty bad and not very memorable. That's not to say I don't like Atlantis: The Lost Empire, Treasure Planet, or Brother Bear, because I do, but after stepping back, really looking them over, and comparing them to what was released during the Disney Renaissance or even The Golden Age of Disney Animation, Disney could have definitely done better.
Before The Princess and the Frog, the only other traditionally animated film released during the 00's that has so far stood the test of time and has become a family favorite was Lilo & Stitch. In between a bunch of films that were mediocre at best with most audiences, it was a huge success for The Walt Disney Company. It had unforgettable characters and an amazingly touching story that most everyone loved, including myself (I'm not going to lie, it's my personal favorite Disney film), and that is precisely the reason why it did so tremendously well and why Disney insists on flaunting its name on television and in the parks. It was the one good movie they had in a series of constant failures, all of which weren't exclusively traditionally animated. Does Chicken Little and Meet the Robinsons ring a bell?
Bolt was Disney's first decent animated film since Lilo & Stitch (I still see plushes of Bolt being sold at the Disney Store and Disney Parks), but The Princess and the Frog was Disney's ticket to success, and with how well that, Winnie the Pooh, and Tangled have done, I don't doubt that we're entering into a new "era" of successful animated features from the mouse.
Anyway... my point is that people want to see good movies, and if it's not good enough to meet people's demands, nobody will see or remember it, regardless of the medium it's presented in. Yes, traditionally animated features such as Treasure Planet, Brother Bear, and especially Home on the Range were panned, but so were CGI films such as Chicken Little and Meet the Robinsons. But, as I previously mentioned, Lilo & Stitch was the "diamond in the rough" so to say and did absolutely fantastic, and things started to pick up the pace after Bolt was released.