There are really only a handful of anime that is popular that I really disliked. The biggest example of that was "The Melancholy of Haruhi Suzumiya", which even saying that name in a forum dissing anime is like asking for the entire world's nuclear arsenal to triple and then fire it all on one location, namely my house. I didn't like it, but a lot of people do. I did not like Strawberry Panic, but some people do. Ghost in the Shell, I found merely alright; many regard it as a classic. It takes all kinds, and maybe the tastes of those particular fanbases are not in line with my own (then again, I am not saying I am very niche, as I greatly enjoy DBZ, Yu Yu Hakusho, FMA, etc. etc).
As to the Transformers 2 example...no, again, just because it made over 830 million doesn't mean that it was good. Could you ever consider that, in fact, 80% of that 830,000,000 regret spending their money? Then it would be an example of popular and bad. Or rather, if a lot of people really hated it, then it wouldn't be too "popular". Popular indicates that it stays in the public mind for an extended period. To this day, people STILL talk about Star Wars, as it has never really left the public mind, and several quotes have become memes or street vernacular. Hell, it doesn't even have to be nearly as big; People are still raving about The Dark Knight as being one of the best superhero films of all time. Transformers 2 was a summer blockbuster that happened to make a lot of money, then kind of died off after 6 months and only got remembered because Dark of the Moon was released.