Aren't micro instances $15/month? (Plus EBS backing, unless you want to lose your DB on reboot.)
Regardless, it's added complexity that you can avoid with MySQL early in your application's lifecycle. Even if it's not much more expensive, you have more hardware to administer. Compare that to a Rails+MySQL stack, which you can run on a single box. (There are added benefits of replicas, sure, but they aren't easier to set up, per se, then just installing your stack on one machine when you're getting going.)
Yea sorry $15/month (EBS is practically free, as is Elastic IP), but anyway my point still stands at $30/month. I think you'd be hard pressed to find a developer who doesn't spend that much on coffee per month (not to mention merchant accounts and support and code hosting and bug tracking and blah blah blah) :)
As to the rest, sure, it's sys-admin-wise easier to setup. But then you have to consider stuff like database dumps/backups. Where are you storing them? Have you tested your recovery plan? Then there's hassle when you decide you need a dedicated db box and move it there (friday fat-finger, anyone?). True enough that none of these are deal-breaker level issues (evidenced by the ubiquity of MySQL/etc).
With mongo you spend a tiny bit of extra money and a tiny bit of extra time setting up a replica set which handles your backup for you. And then when you need more db horsepower you just start sharding or just adding more replicas and sending reads there. Need to upgrade the db box? Cool just add a huge instance, add it to the replica set and promote it when it's done syncing.
I certainly agree that it's a trade-off... it's just one that I think is not driven by data durability. Either way I need to handle my disaster recovery with some kind of automated system and I'm just suggesting that whether this is some kind of cron-job, restore recipe, etc backup of a db-dump or a replica on a cheap extra box is a wash.
Regardless, it's added complexity that you can avoid with MySQL early in your application's lifecycle. Even if it's not much more expensive, you have more hardware to administer. Compare that to a Rails+MySQL stack, which you can run on a single box. (There are added benefits of replicas, sure, but they aren't easier to set up, per se, then just installing your stack on one machine when you're getting going.)