This is one of the main reasons I've stuck with the machines. I have a rotator cuff issue in my left arm that makes that arm very unstable. Lifting heavy things with that arm without any support makes me very nervous, even after doing PT exercises for 4 months.
The reason for this is because many machines have a set path and range of motion. Because not everyone's body is made the same, this can cause problems down the line since the movements are not natural. You are also recruiting less of the smaller muscles in your body that help with stability and balance, while only developing the larger/dominant muscles. I believe that to truly be strong you must train all your muscles to work effectively as one system.
Obviously limitations from injuries are extremely specific to the individual, so your issues may legitimately cause some barbell lifts (particularly bench presses) to be a bad idea. But I do also personally know of a lot of anecdotal evidence that points to freeweight exercise reducing the impact of people's injuries: e.g., knee pain from squats in a smith machine disappearing when performed in a power rack.
In general, you should mix cardio work with lifting heavy things. The ratio will depend on your goals, as will the kinds of lifting you do. All things being equal, exercises that involve more muscle groups and larger ranges of motion will burn more calories than isolation lifting (which is what most machines are set up to do). If you have weak joints or other physical constraints, machines can be a good place to start, as they will provide you some degree of support and help with your form.
Part of the reason you hear about so many methods is that so many of them work. Most are greatly oversold, and in the long run you'll find out what works best for you and ignore the cookbook-style exercise plans, but anything that motivates you to create a fitness plan and stick to it in a disciplined fashion is a good place to start. In fitness, consistency creates more progress than efficiency, and premature optimization is still the root of all evils.