What to do when the professor does not stand up to cheating?
Beer and Circus calls this the "student-faculty non-aggression pact":


Faculty provide an easy class and don't look too hard into cheating
Students happily take the easy grade and leave the professor free to do research


I wouldn't say this is "the rule"; plenty of faculty do an awesome job teaching. But, I'm not surprised to hear your report -- some faculty don't care about teaching generally, while others care about teaching but don't care about grades or catching cheaters. Many feel (for better or worse) that cheaters get what they deserve eventually, and don't want to be personally involved in punishing them. 


  What to do...


I would carefully check the department and university policies -- often, cheating cases are explicitly prosecuted "at the professor's discretion." I would also speak directly with the professor. Speaking of....


  I started assigning zeros to the offending students...[collected evidence]...and deposited the six-inch-tall stack of documents at the professor's door.


I suspect this was not the best way to go about it. I would recommend first speaking with the professor, making them aware of the problem, and asking how to proceed. At a minimum, this could have saved you a week's worth of wasted effort. As it is, you assigned a bunch of zeros, and it sounds like your professor was okay with this -- that is some punishment, at least. 


  Is this just [the way of] academia?


Well, it's certainly a bit dysfunctional. And it's inevitable as long as prosecuting cheaters is a lot of work for the faculty while providing absolutely no "reward" when done successfully.