As an anecdotal counterpoint, I'm an extremely happy Name.com customer. I transfered several domains to them a year or so ago from GoDaddy. They support two-factor authentication, their interface is uncluttered, I pay them less money than I paid GoDaddy, and I haven't had a single issue. I would highly recommend them to anyone looking for a registrar.
That being said, I don't use them for DNS. If this is a feature of their nameservers, I do find it strange that they don't offer a way to opt out (other than using alternative nameservers).
This is what initially drew me to name.com, they seemed to have their act together. Unfortunately there just isn't a way to fully evaluate a situation without trying it first.
Just as I don't give GoDaddy business any longer due to their poor corporate ethics, I can't recommend name.com as a registrar because I must take into account the way in which they run the rest of their business. I will be ceasing my relationship with name.com as soon as reasonably possible.
That being said, I don't use them for DNS. If this is a feature of their nameservers, I do find it strange that they don't offer a way to opt out (other than using alternative nameservers).