Here is my story why I tried dnscrypt: https://medium.com/@nykolas.z/ending-dns-hijacking-with-dnsc...
For example, consider that Cloudflare proxies about 10% of the Internet. Well, if you request a site they proxy, and DNS is in the clear, it's obvious who you are connecting to.
But if you request a site and the DNS is encrypted, you could be visiting any one of 10% of the sites out there.
Similarly, if hosting on AWS or Google Cloud platform, there's a LOT of other services hosted in those IP blocks, and IPs change frequently, so there's a significant degree of ambiguity.
This is all in addition to fixing the threat of DNS leakage for VPN/Tor connections.
... and strips SSL off on their side, so 10% of internet is, in fact, MITMed.
(:
If you choose either of the latter two options, bad guys can't MITM you, the middle option has the benefit that they can't even MITM you by subverting a public CA (since only CloudFlare's own certs are trusted) the latter option has the benefit that you can "just" switch off CloudFlare and your site now works as an ordinary HTTPS site with no changes, if you ever want to do that.
https://stackoverflow.com/questions/22775065/cloudflare-add-...
It's just my gut feeling, that CF might abuse its unique position, having access to large part of internet traffic in plaintext. What other CDN gives free services? Hint, why Google Analytics is free?
One certainly can argue against Cloudflare specifically, or against centralization in general, but IMHO "they see traffic" isn't a very useful argument on its own.
So yeah - it mostly only matters for VPN/Tor traffic.