Filtering on the time capsule?

Yes. Put the files you DON'T want backed up in Time Machine's Exclude list.

Is there a way to set up the time capsule to only back up certain files, and not others?

As Kappy has advised, you may have to think about things in a different way to understand Apple's thinking with Time Machine.

The basic thinking is that you want Time Machine to make a complete back up copy of your Mac......in case your Mac's hard drive fails.

Once you replace the hard drive on your Mac, you can restore your Mac back to exactly the way it was before the drive failed. Of course, this would not be possible if you are excluding files from being backed up.....since your Mac can only be restored with the files that have been backed up.