Most freemasons are there by force and have been saved from a prison sentence so to speak to join them
its hinted that neo in the matrix is not a very honorable person and has something legal or deviant on him that morpheous and trinity know about like for example child attraction or something really weird when trinity says "be honest he knows more than you can imagine" kinda alludes to the fact that the ONe is actually not very worthy of all the prestige like he killed someone ages ago or something or downloaded a lot of child porn