We make things more annoying for VPN traffic because it's 99% bad actors. Every time someone is up to no good on our services, they're behind Tor/VPN.
It's simple cost/benefit analysis. If you think a business should bend to every single whim someone might have, then you haven't built much of one.
Making someone run Javascript so they can click on a captcha? Worth the loss of a few pennies because someone's angry about it on HN.
You need to conveniently ignore why people use Cloudflare to say that Cloudflare is breaking the internet. Ideally, nobody would have to use it, but that isn't reality.