There's no way to know for sure, but Fox's Megyn Kelly tried to put it into perspective.
Using a "rough estimate," Kelly divided the House Judiciary Committee's total budget by the number of hearings during this congress so far and comes up with a "crude measure": $125,000. (Relevant section starts 7 minutes and 55 seconds in.)
To be fair, we can't say that Colbert directly cost the taxpayers anything -- and the Committee's budget goes to much more than hearings. But if even a "rough estimate" has each hearing at $125,000 and the number is actually lower, it still begs the question if a comedy routine in the midst of a serious hearing is worth it.