I realize a couple of basic differences between the two, i.e.
EC2 is going to be cheaper
RDS I wouldn't have to do maintenance
Other than those two, are there any advantages to running my database from RDS as opposed to a separate EC2 server acting as a MySQL server. Assuming similar instance sizes, are both going to run into the same limitations in terms of being able to handle a load?
To give you a little bit more info about my use, I've got a database, nothing too big or anything (biggest table 1 million rows), just high SELECT volume.
This is a simple question with a very complicated answer!
In short: EC2 will provide maximum performance if you go with a RAID0 EBS. Doing RAID0 EBS requires a pretty significant amount of maintenance overhead, for example:
http://alestic.com/2009/06/ec2-ebs-raid
http://alestic.com/2009/09/ec2-consistent-snapshot
EC2 without RAID0 EBS will provide crappy I/O performance, thus it's not even really an option.
RDS will provide very good (though not maximum) performance out of the box. The management console is fantastic and it's easy to upgrade instances. High availability and read only slaves are a click away. It's REALLY awesome.
Short answer: Go with RDS. Still on the fence? Go with RDS!!! if you enjoy headaches and tuning every last little bit for maximum performance, then you can consider EC2 + EBS RAID 0. Vanilla EC2 is a terrible option for MySQL hosting.