I use a gator bass pedal bag for my bongos. It has a side pocket that fits my bell, sticks and wrenches as well. It's thick padding with soft interior, but super protective and very portable. The main thing you want to protect are your heads. Always take the macho down a few turns after playing or if you are gonna store em' for any amount of time. The hembra I usually leave right where it is. Believe it or not, throwing one of those thin nuskyn synthetic head on the macho works really well. But I digress.
If you really want to save money, just find a small gym bag and throw a pillow over the heads.