Yeah they have a few products (e.g. EMR, RDS) where they charge by the instance anyway so you're just paying them by the hour for the five minutes it would take you to set up the server once
Hmm. I think you underestimate the effort that is spent on those two. RDS has really good replication which is really hard to configure and set up yourself. And having configured Hadoop I know it takes more than 5 minutes :) Perhaps Whirr makes that easier. Also, EMR's Hadoop is tuned to work really well with S3, which you don't get with stock Hadoop (or even with Cloudera's).