First off, I do understand most of the hatred for both Flash animation and CGI animation. In the case of both, especially CGI, it's mainly because of nostalgic people who grew up with the 2D animation of the 80's and 90's, as well as how prominent it is anymore, combined with the money that's spent on both kinds of animation.

I should tell you that Flash is but an animation tool, not a medium like people have seemingly been lead to believe. If Flash is used correctly, you can do great things with it, just look at My Little Pony: Friendship is Magic for example if you want to see what Flash is capable of doing. It takes time, money, and skill to do something with Flash, the problem is that it's so cheap to animate with it, hence why a large amount of Flash animated cartoons are hated.

As for CGI animation, again, like Flash animation, you can do great things with it if it's used correctly, otherwise it can end up being a disaster. The reason CGI is often hated, however, is because of two things: One being that people who grew up in the 80's and 90's watching 2D animated shows aren't accustom to it, and bash on it in the name of nostalgia, the other, probably larger reason is that it's overused to death anymore since it makes the most money of any animated show or movie in recent times.

Outside of animation, a larger contributing factor is the writing of Flash and CGI animated shows and films, again, if you spend time and money on it, you can come up with something great, otherwise it can end up being hated by many people, and that would be a problem.