I think more than anything it is the nickle-and-dime frustration of being charged multiple times along the way. It would be more like if McDonalds charged per bite instead of per sandwich. Even if the final bill isn't much different, it changes one's eating habits and likely makes the whole experience less enjoyable in the end.
With Unity, users don't like the new labrynthian TOS. It doesn't help that multiple times people have said "I need to pay if I release a free to play game?" And Unity has clarified "no, that isn't what we meant, you won't need to pay for those." It is either on the Unity legal team for writing the terms so poorly or the marketing team for translating them poorly. Either way, trust has been lost. If Unity builds in a legal back door to charge later for phantom installs or retroactive usage or whatever, that makes an operational risk that devs might want to avoid.
Also, separately, the masses will send idle death threats for nearly anything. Given a large enough consumer base, idle death threats will be sent for any change (even a positive one) or no change at all. I'm guessing that McDonalds' CEO doesn't make noise about it when it happens.