1. My domains all predate Amazon becoming a registrar. I registered my first domain in 1997. I register them for 5-10 years at a time. There's no simplicity benefit in transferring and paying more.
2. Too many eggs in one basket. I prefer to minimize (a) the chances of losing an account/asset and (b) the impact if it happens. If Amazon drops me, or has a long-lasting outage, I can re-build everything I run on another host and point the domains there in an afternoon. Not so if Amazon also owns the domains and hosts the DNS.
Not to mention the dynamic alias records, automated certificate validations and auto-renewing, and the very excellent integrations with other AWS services.
People like making life harder for themselves /shrug
2. Too many eggs in one basket. I prefer to minimize (a) the chances of losing an account/asset and (b) the impact if it happens. If Amazon drops me, or has a long-lasting outage, I can re-build everything I run on another host and point the domains there in an afternoon. Not so if Amazon also owns the domains and hosts the DNS.