I also have rarely seen or heard of any issues (even online after-the-fact) of people complaining about pets on their flight. Granted, I'm not exactly seeking them out, but if it was an issue for most passengers people would be complaining and it probably would be something that wouldn't be allowed.
Furthermore, the tests that I've heard of on the Amtrak pet trials have resulted in very few to no complaints. Due diligence is required, but assuming that it will be the source of tons of complaints and almost assuredly cause a lot of issues is, frankly, an assumption too quickly gotten to.