I don't think anybody would try to suggest that machines don't work the muscles. Of course they do, as you quite rightly say. However our bodies work in a chain of connecting muscles, joints, and other bits (as you can see I'm not being too scientific here!).
Using a leg extension will undoubtedly strengthen the quads, but if you only strengthen the primary muscles and nothing in between, this is not how the body works. Which is why, for example squats would be a better general excercise as it works the full leg to various extents, as well as the arse, and the core.
You may well lift more with a bench press machine, but doing a free weight bench press at potentially a lower weight will (in my opinion) be a better exercise for your body overall. I would suggest that doing the bench press with free weights has pinpointed somewhere in the chain where you are not strong enough to lift heavier, and you are just bypassing this by using a machine all the time.
I certainly use machines to target individual muscles occasionally, but your day-to-day set of exercises are probably best off being compound type movements with free weights where possible.