Why Isn't the SQL Server Agent Service Set to Automatic Startup by Default?
During the install process for SQL 2008 R2 it gives you the option to change the start-up type.

I can see a slight desire to not have it start automatically depending on what you might be using it for. I have some setups that the user has some Agent jobs that clean up data or immediately start processing data. If I am troubleshooting, or in general the server goes down, I may not want all that processing to start back up immediately after bring the server back online.

In most instances though you will see the Agent set to automatic start up.