That isn't mentioned in the linked article at all - they just say "free".

However, if you go to the actual API site: https://fisync.dwolla.com it does say the same cost as an ACH transaction.

I believe what they're implying is that what's free is use of the infrastructure but each transaction through the infrastructure incurs a fee. Contrast that with a CC payment gateway where you're paying $30-$40 per month in membership fees regardless of whether you even process payments for a given month.