There's a fee of $0.50 per hosted zone and month for Route 53, in addition to the $0.40 per million queries. This is optional if you don't want to use Route 53 for DNS, so you can still use a free option like Cloudflare instead.
Most registrars would reach out & ask you to pay for premium DNS after some sort of soft limit anyways. Companies like Google pay thousands for their DNS. Free DNS is a form of over-selling. Cloudflare also has a history of shutting of people's service after they hit some soft limit, and asking you to upgrade to paid.
I've had that talk with cloud flare. They didn't come over very aggressive and confirmed that I wouldnt have a issue when I stay on free.