I don't think a lot of the ire is misplaced. A lot of it came from the introduction of Amazon searches and marketplace suggestions. While at first it was just a privacy concern and a bit of a middle finger since there was really no word on it happening, no notice on their website, etc... you could at least remove it, easily. But in later versions they've since made removing it next to impossible without breaking the dash as a whole.
Now, I'm not saying they can't have it, or even that they can't default to it being on. But at least tell users beforehand that it's going to be there and at least provide a relative easy way to disable or outright remove it completely. Just doing this would make a lot of people happy. At the end I agree that it's Canonicals operating system, and they can do with it as they wish, but if they're going to pull stunts like that then don't cry when people don't like it.
I'm the same way when it comes to Windows 8/10 and how they did the same thing with searches and trying to force the metro screen which preferred Applications from the store over standard programs.
I'm an Arch user and ended up favoring DWM after Gnome 2 got ditched, was kind of forced into it since I didn't like XFCE and never been huge on KDE ( too many options, often times makes finding the one you want more difficult, downsize of being too open ). I actually LOVE Unity. Honestly, there's not much I don't like about it and I like the newer features that they've added with the integrated menus and always showing them... But that aside my biggest gripe that I can not get over, is my more recent distrust over the forced Amazon stuff and store integration's in the dash. It's an absolute deal breaker for me ( and I know for many others too ).
I agree that Ubuntu is one of the biggest names in Linux right now and likely our shot into mainstream... but at what cost? If we let Ubuntu get away with such things, how much further are they going to push it? If they get so strong that they reach the mainstream with the knowledge that we'll bend over and take it "just because", then that pretty much gives them the go-ahead to do whatever they want.
And if they aren't willing to take the criticism and use it, then they shouldn't be able to move forward, at least not as a free ride from the fake praise of Linux people just to see it move forward.
Now, I don't personally think Ubuntu has or is going to make as much help to Linux as Steam is. Steam, I think right now is the big player that opened up the floodgates to having more people ( at least, casual gamers, and even a few AAA games ) be able to stay on Linux.