You might search for rubber flooring for gyms with recycled content. There are roll-out and tile options. If you like a more industrial look, there are also floor tiles for garages that might have a green option. Not sure of your budget, but when I looked into it for my basement, there were pretty reasonable prices available. Plus, it's durable. You could pick it up and take it with you when you move and find another use for it.

Flor carpet tiles.

http://www.flor.com/

Oops, I hit submit too soon. I forgot to say that they are also recyclable themselves. You can get a catalog sent to you, there are lots of good ideas in it, and you can also get samples sent for a small fee.

If you're planning on staying for a while, I'd recommend float-installed bamboo flooring. It takes more effort to install but it is durable, looks nice and a snap to pull out (assuming you use the snap lock type, glues are pretty toxic anyways) if you want to take it or the landlord objects.

Cork flooring is good if you want to hang around a while and half the price of bamboo.

Another good option I just found is Place n' Go, flooring that snaps together but would be a lot easier to clean than rubber tiles.

Thanks for the great suggestions!

Most of the options I am finding are upwards of $5/sq ft, which breaks my budget for the tiny 48 sq ft space. : (

The rolled rubber is still my front-runner for cost. The 6x8 ft recycled PET indoor/outdoor carpet section was under $30.