If you do commercial SEPA Transfers, yes there are fees. If you only do push transactions (ie, customers sends SEPA transaction to you), it's largely account management fees.
The pull transaction (SEPA Debit) isn't free, you can buy transaction packets (usually around 5-15€ per 1000 transactions) as well as paying a fee on monthly cash inflow (usually around 0.1-0.3%). Honestly, it's peanuts.
SEPA also doesn't mean that the transactions are free, either. According to a third party transfer service (https://transferwise.com/help/15/paying-for-your-transfer/29...) there might still be some fees from banks.