You must be using straight needles? I've never had a needle poke through a bag and I use circs almost exclusively.
Anyway, I use large plastic, zip top bag with handles that I got at my LYS. It's big enough to hold my needles, my bag of accessories, a smallish project, several patterns, extra yarn....
When I fly I don't carry all that. Just my kindergarten scissors, yarn and project and a few extras if needed for the project and I carry them in a Ziploc in my carry on bag. Anything else like extra yarn, needles, etc goes in my checked bag.
If I was traveling by car I'd just carry my big bag of knitting like I always do.