I know I'm terribly late to this thread and it may have already been mentioned...
Regarding making everything free while still drumming up enough money to keep the site running -- I think this place is like all Christian resources. It takes at least some money to run, just like a church building, and it's always a delicate balance of how things will be paid for to keep the lights running, and who should be paying for it.
Should the few pay for the majority to benefit from keeping everything free? And who should the few be who pay, and who should the others be that shouldn't have to pay? It's an age-old question.
To give this site its worthy due, they've tried experiments in the past to try to keep everything free. I've been here since 2009 and have seen a few variations of when they tried running ads to avoid charging members.
However, it seems that they had no way of controlling which ads were shown, and would run into the problem of ads being run that were questionable on a Christian site. (This is very similar to how my Lutheran school was -- they relied on donations from within the congregation and never from the community at large because they didn't want outside influences trying to muscle their way in via money.)
So I really do think the administration has tried its best to be all things to all people, but in the end, some kind of monetary means is still necessary.
The other thing about putting Private Messaging behind a paywall is that it greatly cuts down on the amount of abuse. Back when PM was free-for-all, there were a lot of problems with people stalking others and/or harassing others with inappropriate messages. We used to have a few members who, in the forums, presented only the most Godly of answers and posts, but behind the doors of private messaging, were sending others very inappropriate propositions, resulting in bans that left some people loudly complaining that these bans were unjustified without knowing what was going on.
Now of course, even with a paywall, any of this can still happen.
But I would guess that it really helps to cut down some of the riffraff and makes it a bit more bearable for the volunteer moderators who are putting in their own time for free as it is.