Rand Paul is a declared candidate for President, and the EFF does not make political endorsements, so they're probably trying to avoid discussing Rand Paul too much.
Also EFF Executive Directory Cindy Cohn is a Democrat campaign contributor, supporting John Kerry in 2004. This there is no way they'll do anything to support a Republican. The EFF claims to be non partisan, but when their leadership financially supports political candidates, the logic of being non-partisan is somewhat thin.
If you invested $500 in a company, wouldn't you want that company to succeed? Thus it's impossible to be Jon partisan when you are actually partisan.
And I think you must have a very short and selective memory if you think the EFF has not been taking Democrat leadership (especially Obama) to task over mass surveillance.
Additionally, I believe it is possible for individuals within organizations to hold personal opinions and not use those personal opinions to drive organizational policy. Thinking that everyone must subvert their own honest efforts with some sort of underlying agenda is cynical at best and paranoid at worst.