While I don't know about the EFF's overall argument, as an absolute statement I don't think you are correct here. In the USA at least, "Public Accommodations" (which your cafe example would be) are in fact subject to regulations that limit their ability to discriminate, require accommodations for the disabled, etc., and these apply regardless of whether it's public or private property. Something that is open to the general public is different in law then purely private property (private clubs and religious institutions are specifically excluded from federal law, but that's it). There are also going to be different expectations of privacy and default access levels.

Physical to digital analogies are often a poor match anyway, but in this case I'm not sure even if we accept one that it fully supports your point. Private property open to the public is not legally the same as purely private limited access property in terms of who it may exclude, when it may exclude, and why (as well as lots of other standards).