You may not be able to control them, but you can influence who YC startups do business with. You screen founders heavily based on perceived intelligence, and probably based somewhat on perceived ethics as well. You probably have some sense, before you fund them, whether founders would be willing to do business with the RIAA or MPAA.

You could be doing something to dissuade YC-funded startups from engaging with Monsanto. I think it's a valid question why you're putting significant effort into fighting the MPAA and RIAA, even banning SOPA supporters from demo day, while you do not take a visible stand regarding Monsanto.

Genetic engineering is outside of YC's core competency, but there are strong parallels between trying to exert tyrannical legal control over digital IP, and trying to exert tyrannical legal control over genetic IP. Unlike copyright infringement which at least requires an infringer, genetic IP spreads itself, and embeds itself into other [public domain] IP that was not originally infringing.

Since you've opened the door by taking a stand regarding the RIAA, MPAA, and draconian copyright laws, you shouldn't be surprised when you get flack for being silent on other issues: Monsanto, companies (including Monsanto) directly involved with the drug war... perhaps even private security contractors which operate in war zones, the private prison industry, big pharma, or environmental polluters.