Why do you suggest that machines aren't good for strengthening muscle? I have and use a Bowflex machine and have had good results with it for the past few years. I prefer free weights for a number of other reasons, but the Bowflex is a good, safe alternative for me. Please explain when you have a chance. Thanks.
I think most machines are a poor substitute for freeweight exercises. What I was talking about particularly was about increasing bone density and the strength of the joint tissues. For instance, I have seen studies that show better bone density gains in the leg and spine from squats vs. leg presses. This makes sense because in freeweight exercises your bones and joints are actually holding up weight and controlling its position in three planes of movement, from the time you pick it up to the time you put it down. It is putting more and more varied stress on the tissues, so they adapt by getting stronger. Moreover, if you use good form, it is the healthiest kind of stress because it is most similar to what you actually need it for: standing on the ground, pushing weight up over your head, squatting, lunging, etc...
Most machines fix one or more planes of motion. The worst, like Nautilus machines or a leg extension machine fix everything, so you are merely pushing a lever along an extremely limited track. Actually, I take that back, the worst is the Smith Machine for squats, which force your upper back to move along an unnatural path with your feet fixed on the ground. This multiplies the shearing forces on the knee, as do leg presses. The idea that such machines are better than free weights for rehab is silly. They may be useful after a surgery or something really severe, but once you are strong enough to do a basic free squat with bodyweight, they should be phased out. The idea behind rehab and conditioning should be to get damaged or weak parts functioning properly as soon as possible. It makes far more sense to do this using complex functional movements right away, rather than building up strength in weird artificial patterns then trying to transfer it over to functional patterns.
Pulley machines are a little different, in that the handle you pull on has some freedom of movement, but still are not as good as actual weight, either for functional strength or injury prevention, which are two parts of the same thing. I consider many of the weird freeweight exercises I learned from magazines and books when I was a kid in the same category.
There are a lot of myths floating around in the exercise world, and a lot of beliefs are influenced by commercialism and fads, not science or sensible thinking. The worst such fad has been bodybuilding. Bodybuilding is based on a deeply flawed, oversimplified model of body functioning. It divides up the body into a few major muscle groups, then tries to target those muscles by using "isolated" movements. In fact, it is neither desireable or possible to really isolate a particular muscle. Even the weirdest little dumbbell or machine exercises involve many muscles, and complicated movement patterns, it's just that most of them are not very useful patterns, and some are actually harmful. Bodybuilding has it completely upside down and backwards, and most machines are influenced by this paradigm.
The best exercises are weight and bodyweight exercises. They are based on training general functional movement patterns, not "muscle groups". They are also not that difficult to learn to do properly. Most people don't need extensive training and supervision to do simple standing barbell exercises, dips, pullups and pushups, which provide just about all the options most people would ever need. I plan on using nothing but the ground, an Olympic barbell, a few bumper plates, and a couple of boxes to hold the bar up for plate changing as my entire strength program for the next year. I could teach anyone that has normal physical aptitude enough to get them going on a program with a few simple exercises in minutes. The Olympic lifts require a little more training, but not that much. I learned to be moderately competent at all of them along with partials and supplemental exercises at a 3-day camp.