Transferring those bits with just the right logic for each transaction scenario is what still costs something. I'm sure the margin is massively excessive today. But I don't think it can be quite 'effectively free'.
They're only free in certain circumstances: personal transfers, and only for some bank accounts. It wasn't that long ago that all e-transfers cost $1, which makes them pretty impractical for giving a few bucks to a friend to split a pizza or whatever. Venmo's been around longer than free e-transfers.