As for history being written by the winners, didn't the Simas 'win' the Three Kingdoms with the founding of the Jin dynasty? They're certainly not looked upon as good people (although that's probably more because of how tumultuous the Jin dynasty was and how it ultimately failed).
I view the YTR not as the cause of the collapse of the Han, but rather as the straw that broke the camel's back. There was dissent all around: not only among the peasants, but also among the intellectuals - such as the student protest at the Imperial University and how Emperor Huan handled that (which reminds me of another Incident in recent Chinese history) with the Partisan Prohibitions, which effectively alienated the gentry along with the economic crises and famine and natural disasters that plagued the peasants - and how Emperor Ling did absolutely nothing about it. Like has been said earlier, if it wasn't the YTR, it would have been something else - after all, the Red Eyebrows didn't cause the collapse of the Han Dynasty. Well, not in the same way.
I think the guys viewed as the ultimate baddies in this situation (besides Dong Zhuo) were the eunuchs. They represented corrupt government, heavy taxes, the selling of official titles, and overall sliminess.