They can log unencrypted DNS queries coming from Cloudflare, yes. But they can't correlate those with the incoming encrypted queries, not when the amount of traffic coming in is as vast as it will be. It doesn't help much to know "some Firefox user somewhere tried to resolve such-and-such domain".
Your ISP has access to more detailed data on you than DNS queries. Also CF servers are typically located in the same jurisdiction as your government and send unencrypted DNS queries from there. Now instead of dealing with every ISP your government has to deal with just one company in one location, no need to even ask that company anything, just come in and setup mirroring point, very convenient for the government, not very good for you.