Can't speak for other pools, but for me those payouts are combined earnings from masternodes, PoS wallets and fees.
And it's not really an accurate representations of the fees. There are a lot of miners getting paid in their altcoin of choice but the pool's fee's are always converted to BTC.
The more miners using altcoin as payout will give a false impression in the BTC payouts of the "large fee"
anyway, just a light dusting of FUD on this one but should clear it up enough for you.
thnx