Baleee Dat! Initially I was very intimidated by shell access due to it's power, and thus my ability to wreck stuff. Here's my two cents: start out by setting up a "practice" subdomain under a seperate user account so you don't have to sweat messing up your main domain. Next try a specific basic project, like installing and enabling AWStats or something.
The shell grows on you quickly and in a suprisingly pleasant way. In a few short weeks I went from being strictly Windows to running customized Ubuntu, with a distinct preference for the command prompt. I settled on this after auditioning a few different distros, and don't see myself using M$ in any other context than employer provided machines from here on out. Jump in, the water is fine.
Here are a couple links that might be useful...