He claims he complies with the DMCA.
We won't know until the trial happens, but from what I've read, there appears to be plenty of emails showing the employees explicitly discussing how they actually don't take down content.
None of that is what bothers anyone. What people are up in arms about is:
a) Presumption of guilt. A company which may very well be defensible has been destroyed. If the court agrees with him over the feds he's suffered massive revenue loss at a minimum and there may be no coming back as competitors will scramble to replace him in which case he's lost an entirely legitimate livelihood.
b) Extradition on a global scale by federal authorities for what's basically a civil matter.
c) Jail time threatened for everyone involved in the company right down to the web designer when much bigger and, in the eyes of the public, "just as obvious" misdoings from wall street bankers was rewarded with slightly smaller but still massive bonuses.