I have a rewrite in an apache httpd conf file, that breaks certbot. Is there a way to change it so that it doesn't?

If I understand correctly, you want to redirect all non-HTTPS requests to HTTPS. So I guess your rewrites are in a <VirtualHost *:80> container, for a non-HTTPS site.

Now you want to add another condition, to not redirect Lets Encrypt challenges. I think you're probably using the HTTP-01 challenge, which means you want to not redirect requests to http://<YOUR_DOMAIN>/.well-known/acme-challenge/<TOKEN>. So does the following work?

RewriteEngine on
RewriteCond %{HTTP_HOST} !^www\. [NC]
RewriteCond %{REQUEST_URI} !^/\.well-known/acme-challenge/
RewriteRule ^(.*)$ https://%{HTTP_HOST}%{REQUEST_URI} [R=301,L,QSA]