I use AWS for most things (including Route53, which is awesome), but I actually like not having my eggs in one basket. If something crazy happens with my AWS account, I could always theoretically point my DNS resolution somewhere else. The domain registrar is reduced to an annual auto-bill transaction on my credit card and they don't have any particular technical responsibility for my traffic.
This really seems to make the most sense. It's just a name. An entry in a registry's zone file. It has nothing necessarily to do with your infrastructure (which does not need names to function; even email can work without domain names). A name is just a name. It provides no "availability" of network resources. But how many customers understand this?
The problem that flows from this lack of understanding is registrars (people who sell names, entries in some registrar's zone file) push hard for the "upsell" and succeed get customers to sign up for all these other services that are quite different from registrar services. They are qualitatively different services and require significantly more resources than just selling (renting, actually) names.
This is a good point - for web based companies, your domain registrar will always be your single point of failure. So it makes sense to keep it separate, with the most trustworthy company you can find.
Even in nasty scenario (like GoDaddy's DNS service going down), you can still point your domain somewhere else, even temporarily. But the worst case, your domain registrar going down, leaves you with no alternatives.
> But the worst case, you domain registrar going down, leaves you with no alternatives.
Your domain registrar does not do anything except mediate your ability to alter your DNS records and allow you to renew your domain name entries: it really shouldn't matter if they go offline unless they go offline for months at a time.
You thereby should never, under any circumstance where your domain's availability means anything to you at all, allow your domain name registrar to handle all of your DNS records (as many of the people in that "GoDaddy's DNS Service is Down" thread have done).
Instead, at least some of your authoritative DNS servers should be hosted by anyone other than your registrar: otherwise, you can end up in the situation where all of your DNS goes offline and you can't update your DNS records.
(Of course, you should really not have all of your DNS records hosted by a single company that doesn't have any internal redundancy in the first place; this criteria alone should exclude companies that don't really care about DNS, like any registrar ever, from being your only DNS provider.)
(Note: I'm not certain if today's outage of GoDaddy's DNS infrastructure affected anyone's ability to use their portal to update their DNS records, but one could easily imagine simple scenarios where that happens.)