It's generally better to work out with free-weights because of the stabilization aspect, yes. Saying that Free weights are better flat-out is wrong in my opinion. Every piece of equipment in the gym is a tool if used effectively and at the right time. Your "core" program will be done with free-weights yes, the other equipment is great for auxiliary uses that compliment your program. Machines are great for end of workout sets because you're likely already fairly fatigued and form may be compromised. You can get that little extra by using machines to ensure perfect form while also safely adding that extra stimulation for the muscle groups being trained.