You’ll want to uncomment those lines again - they tell the web server: “if that file or directory exists, serve it, otherwise redirect to index.php.”
Try putting a test file with some random content in public_html/.well-known/acme-challenge/ and try to request it via HTTP (using your browser or curl). Maybe that’ll show you what the issue is.
Would you mind sharing the domain so I can take a look at the response of your test file? PM would be okay too, if you don’t want to share it publicly (though you should know that all certificates issued by Let’s Encrypt are published to public Certificate Transparency log servers anyway ).
For anyone else reading this thread or finding it via search:
It turned out to be an issue with one of the subdomains and CloudFlare in Full SSL (strict) mode. @curt had a valid certificate for his main domain, but not for one of his subdomains, which caused CloudFlare to show an “Invalid SSL Certificate” error page instead of serving the challenge token. Switching to Flexible SSL temporarily seems to have fixed this issue.