I bought a really inexpensive zippered pencil case at Target during 'back to school' sale time and it works great. I think I paid about $2 for it. It's large enough to hold my 60mm cutter, my 45mm cutter, spare blades for each and a pair of small scissors.
I don't worry so much about stuff flying around in my car (I keep it pretty empty), but more about reaching into my bag and getting cut - my 45mm cuter is the kind that auto-closes when you let go of it, but if it's just shoved in a bag with other stuff the handle can get pressed and expose the blade. Plus it's just more organized that way.