I'm not sure if anyone has posted something like this before but I was recently given an e-cig case by someone who thought I'd find a use for it...I did
The case is fairly hard on the outside and closes with a zip, on the inside there are a couple of elastic loops and a little net basket. The loops are a perfect size for 2 pens which means you can carry at least 4 pens or 6 at a squeeze. The cases can be picked up on ebay pretty cheaply and offer more than enough protection for carrying pens about, the case I have can comfortably hold a Lamy Safari AL with about 1/2 inch room above.
I think with some customisation these cases could be cheap but sturdy options for carrying pens.