All you have to do is look around at the people who use mostly free weights or mostly machines to decide which should make up the bulk of your routine. The people I see moving from machine to machine are usually clueless and/or fat people who always do the same machines and always look the same from year to year.
Sure, I see big guys using machines, but that's usually after doing a lot of free weights. For years, I worked out doing stupid shit while watching the big guys do stuff like weighted dips and chin-ups... and it never clicked until about a year ago.
Is this really true? Take an exercise like the bench press. Would you really rather have a person using a chest press machine using huge weights? Sure, you get stronger in that plane of movement and you may be less likely to be hurt in the gym.
However, I feel like it would be more likely that the person would be injured doing other activities such as sports, because the person's muscle development has surpassed their stabilizer, tendon, and connective tissue development.