I think for a lot of people, they _want_ to see Reddit not as a "company trying to be profitable" but more as "the de-facto community message board on the internet" where everything is free, open, and equitable. Shutting down third-party APIs makes the site less open in a lot of ways, which is rubbing people the wrong way.

That being said, I do agree that they own the API and have every right to charge for it. I am going to be very disappointed that my preferred way of browsing Reddit is going to stop working, since the official app is not a great experience.