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Spam filters are discrimination, but I don't see anyone suggesting we stop using those.

Then go after the site owners who choose to enable this.

Isn't the problem along the line of so many different people using effectively the same IP addresses (exit points) and looking somewhat similar to each other?

I'd imagine if there was a major ISP network out there that was doing NATing or similar for their customers so everyone came from a small set of IP addresses they'd get the same treatment. More users on the same IP means more abuse from that IP. If anything Cloudflare isn't discriminating. To handle Tor users better you'd have to discriminate (technical definition, not the negative form) to handle Tor users better