I agree that they don't fit in well with the standard American left-right spectrum, and agree that they are closer to libertarian than liberal. But yes, I think they are perceived to be in similar position as the ACLU: somewhere to the left of the left. While in theory both of these organizations might be embraced by conservatives as protecting constitutional rights, in practice both are "liberal causes".
An odd citation, but appropriate considering I'm arguing about perception rather than reality: "The Electronic Frontier Foundation (EFF) is a liberal and libertarian organization which promotes the protection of personal rights on the internet, particularly privacy and free speech. Category: Liberal Organizations"
http://www.conservapedia.com/Electronic_Frontier_Foundation