There was a great program on WNYC recently about "Why Classically Music Has Become More Abstract Through the 20th Century" and there were interviews with people like Milton Babbitt who had some pretty insightful things to say. Mostly like - popular music has become so much simpler and legit music has become so complex that it is harder for a listener who has had no exposure (much less training) to contemporary avant garde classical (CAGC for short from now on, OK?) to actually HEAR what's going on. If you have no construct for what you are listening to, then it becomes a product of how much you hear can be "forced" into the boxes of what you CAN hear.
The stretch from Bird to SHAPE OF JAZZ is not that big, really. Especially when you look at some of what Dolphy was doing over standard harmonies and form. But FREE JAZZ isn't based on that model at all. So you got to dig into it (if you feel like it, like SAM'L says, no music police coming around to take your axe away) almost as if you were playing, how does the big aural picture look/sound, be a little academic til your ear starts to catch up.
I'm wit Paul though, kind of an in/out guy. Anytime I play in a free situation, I've got the same set of ears on the side of my head (well, sides of my head) that I do when I'm playing standards. So what you play should in participation with the aural environment you are in.
Personally, being an in/out kind of guy, I really enjoy the possibilities opened by cats with non standard approaches, cause as soon as I get'em in my ear, I can use'm playing whatever I want.