Transaction fees are currently kept by the pool.  Their total value tends to be a small fraction of a percent.  Of the ten most recent blocks, the largest txfee included was 0.036 BTC, which totals 0.07% of the total block reward.  One block had no fee, some others had less than 0.001.  The pool currently PAYS txfees on payouts when bitcoind decides a fee is applicable.  At least for the time being, the pool is paying more in txfees than it collects (but that is changing as more users use automatic payouts).

I have been thinking of how to handle txfees the mining reward decreases (or the txfees drastically increase).  My current plan is to run a counter that keeps track of the txfees the pool has earned over the course of a difficulty, and then allocate that total over all shares submitted that difficulty once the difficulty changes.  I haven't put any effort into it yet due to the currently negligible amount of txfees being included in blocks.