FathomDB is much closer to Amazon RDS - MySQL-as-a-service. Every customer gets their own MySQL instance, and accesses it over the MySQL protocol, using normal SQL (the MySQL flavor at least). Database.com looks to be Salesforce repackaging their wrapper which lets them do multitenancy in Oracle. You'll be stuck with what the wrapper exposes, which isn't very SQL like, and certainly won't be a drop-in replacement for any existing SQL applications. They aren't offering Oracle-as-a-service.

In terms of latency, Amazon RDS and FathomDB both target applications running on the same cloud as the database. I would imagine that would be the sweet spot for database.com as well, but there are some applications where the Internet latency could be tolerable.