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The whole reason for this mess is that VCs refused to invest in his "legal" startup (didn't want to waste money on compliance costs?) and invested in a bunch of "illegal" competing companies instead.

It's regulated by criminal law, not civil code. The complaint quotes the law:

"Whoever knowingly conducts,controls, manages, supervises, directs, or owns all or part of an unlicensed money transmitting business, shall be fined in accordance with this title or imprisoned not more than 5 years, or both."

Presumably if individual Facebook shareholders had real influence over Facebook's actions you could sue them. I would guess the justification here is that YC's partners/etc have a real, tangible influence on the companies they invest in so they do bear some share of the responsibility.