Years ago I got a full shoulder separation in a Judo tournment that basically ended my Judo competition career. They pretty much had to sew my shoulder back on. After about 6 months of recovery, no major problems for years, then as I've gotten older, I've learned that I just can't do flat bench barbell presses anymore. Fucks up my right shoulder rotator cuff bad. Have a problem with it in some other things also. I can do flat dumbbell presses, and can do them on the smith machine.
In my earlier years I used mostly free weights, and mixed in a lttle machine stuff occasionally. I totally understand the deal about needing free weights to get the stablizer muscles involved. I use a combination of both, and for a guy over 60, am doing pretty good. I never competed (in BB'ing) and originally got into AS mainly because all the national level Judo competitors were on. (I was at the national level for a few years). Anyway, just thought I'd throw in my two cents. I think everybody who posted has a point. I think this is one of those things that somewhat depends on each individual. your body, your age, what you are trying to do with your training (competing, just trying to stay big and in shape, sports, etc.) However, it would really limit my workout if I didn't have the machines available.
Like someone said, also sometimes at the end of a workout, I can squeeze a few sets in on a machine that would probably be risking an injury to try with freeweights.