The theory is that by lifting free weights you are strengthening not only the primary muscle, but also the stabilising muscles, joints, ligaments, etc, which all assist the main muscle when you lift.
By using machines you are often isolating the one muscle and not strengthening any of the connecting muscles, ligaments, etc.
For example on a bench press you work the chest, but your shoulders, arms, core, and even your legs to a small extent are stabilising you. If you use a chest press machine you are probably taking a bit away from the exercise.
There is also a theory that using a machine forces you to follow a "fixed path" for the exercise, one that might not be natural or comfortable.







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