There's nothing "Masonic" or suspicious about any of that.
"Fellow traveler" means a sympathizer with a political movement. It usually refers to Communism. The dyne.org people are a bunch of lefties, so that's not surprising. Regardless of their political beliefs, they've been putting out free software and Linux stuff for a long time, and I've never had any reason to be suspicious of them.
Follow the white rabbit is a reference to the first Matrix film.
The logo is a tunnel. Because internet traffic in heads is tunneled through Tor.
