My question would be, are individual Dwolla accounts protected on a per depositor basis? Or, is it just Dwolla Corp's own bank account which is protected under FDIC. Their website doesn't make that clear.

It's entirely possible that user funds are stored in a bank account, owned by Dwolla, and that bank account is FDIC insured. If that's the case, then that bank account is only insured up to $250,000 USD.

They are "not a bank" so that FDIC insurance doesn't apply to you it applies to whatever bank account they are using to hold everyone's money. If they go bankrupt I am not confident I could get my money back.