I can't speak for everyone, but for me it was how far back he set the Marvel Ultimate Universe. Prior to him the Ultimate line had some of the best books out there. Ultimates 1 and 2 (AKA The Avengers) were almost single handedly what brought the Avengers back into the spotlight. And then Jeph Loeb comes in and writes Ultimates 3. That's the day Ultimates fans all around the world cried. Characters were written out of character. The story didn't make sense. Doom was somehow the villain at the end even though he didn't show up until the LAST PAGE. And then came along Ultimatum. The next big Ultimate event.
It. Was. Balls.
This is what set the entire Universe back. Years of work, including some of the best stories Marvel had been writing at that time. And Jeph Loeb set it all back in FIVE ISSUES. I'm not going to go through all that was wrong with it since there's really too much. But I'll leave you whit this list of deaths unnecessary deaths that happened. Again, all in five issues. http://en.wikipedia.org/wiki/Ultimatum_(Ultimate_Marvel)#Deaths