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.
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From the site — "same price as an ACH transaction" — so a few to tens of cents per transaction.
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.