Store homemade kefir with paper towel on top or close the lid normally?
If you'll drink it quickly, you can store it with an airtight lid, but this will make it "fizzy". Personally, I'd store it with a breathable lid to avoid carbonating it, and possibly causing it to explode. There's still live/active cultures, even when you remove the kefir grains.

Edit: quickly, as in a day or so