Are ddos attacks a common enough occurrence to warrant putting half the internet behind ddos protection? In my impression you need to do something really wrong to deserve one.
I actually agree with your overall point as I try to use Tor for a lot of "normal" browsing, but I'm not sure what the correct solution to accommodate both is. It's a hard problem, and having been in that position myself I have a hard time faulting small website operators who have no alternative defenses.
e: just to add to this, I see the existence of ddosing as a significant driver towards centralized monolithic services. If your blog on Palestinian rights or whatever is getting hit, that's an incentive to move it to a platform that takes care of networking for you. It's a little absurd to go all-in on decentralized self-hosting without at least an acknowledgement that with current tech and typical personal-computing budgets, doing so is giving a heckler's veto to literally everyone. Cloudflare isn't the only dimension things can be centralized along.
Do you pay a variable amount for your hosting? How and why? All VDS and dedicated server offerings I've ever seen are fixed amount per month. And more often than not the network is limited by speed, not by data transfer.
Mind you, I see your point and I generally don't like the captchas either, but it is definitely a trade-off and I won't blame webmasters that use the DDoS protection.
One bot that's just stuck on a loop or being overly aggressive is going to have one IP.