I don't get it?? In the newbie forum most especially, pools without fees are preferred over those that take back a small fee.
Here's how I see it: Pools with fees are more reliable in the long run because they have some extra funding to keep their services up and running. Ones which do not incur such fees don't seem to have this safety net.
Am I missing something?
Almost all pools keep the transaction fees. Depending on the number of blocks a pool gets; that might be sufficient to pay the colocation for the server.
So you've paid for the colo. Who runs it? Who maintains the pool 24 hours a day, 7 days a week, and is on hand to respond to queries and complaints in a timely manner? Should a pool op do all this for free?
ALL pool have to be run at a profit or you end up with an unreliable pool. MTRED for example is a fee free PPS pool - not only does the pool op not take a fee but he runs the risk of not being able to payout a run of bad luck.
Whether the pool runs for a fee or accepts miner donations for added services and benefits, there has to be a revenue stream or the pool op has no real way keep uptime high or develop new technologies that help miners even more.
Block tx fees are atm insufficient to use as pool revenue and as the block reward halves many pools will pass block tx fees to miners since they will start to make a larger percentage of earnings.
tl;dr
If you don't want to pay a fee (or a donation) to reduce your mining variance at a pool, you have three options:
1. Stay with fee free pools that don't reward/encourage donations and deal with poor uptime and unreliability
2. Use p2Pool
3. Solo mine and deal with variance.