But what's the counterfactual? People use cloudflare because they want protection from ddos attacks and bots. If cloudflare didn't exist there would probably be similar measures.
Point being, it's a commercial subverting the Internet from inside, reshaping it to better serve the interests of commerce. It is indeed protection, but it's accomplished by reducing variance. 99% of legitimate commerce on the Internet follows the same patterns, use a small subset of possibilities offered by the technology - so why not just block the remaining 1% that doesn't fit and call it a day? It will stop most of the threats to running businesses on the Internet. The 1% of legitimate commerce that doesn't fit the pattern? It's not being ignored per se, just pressured to adapt and conform to the majority.
What is being ignored is that the Internet is not just a place of commerce, and non-commercial use cases, ideas such as empowering people to better their lives, are gradually becoming impossible, as fundamental Internet infrastructure becomes inhospitable for them.
Some of us still remember the Internet being more than just a virtual mall, and are unhappy about it gradually becoming one. And it's not like CloudFlare, et al. are hostile to non-commercial interests as a matter of principle - it's just out of scope for them.
Your second paragraph talks about other (non-commercial) sites. I think I'm missing the link here. Why would the admins of such sites resort to Cloudflare if 'fundamental Internet infrastructure becomes inhospitable for them' by making that choice? They could very well choose to implement their own or no measures at all.
I think the issue is that the general threat level has massively increased compared to the past - not in terms of sophistication but frequency/scale. But that's a consequence of widespread adoption, nothing Cloudflare in particular is responsible for.
Marketing and free tiers.
But my point is that Cloudflare is addressing threats that predominantly affect businesses, and does so well, but the way it does is effectively changing the whole Internet to be more hospitable for commerce, and less hospitable for any other kind of use.