Yeah, I'm in this position. I've been using the machines at my gym (more for variety than any other reason) and when I started looking into strength training, I was swamped with competing methods, many of which instantly sent up red flags in my brain reading "SCAM".
It's difficult for someone from outside the fitness world (me) to judge whether a method is legitimate or if it's simply the fitness equivalent of a get rich quick scheme.
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.
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.
Lift heavy shit over your head. Put it down. Repeat.
To this end, barbell training is pretty much the gold standard in gaining strength. Machines are suboptimal in that they stress muscles in isolation from one-another, and remove the need for compound, coordinated muscle contractions that occur in literally every situation where you would want actual strength. Proper barbell training with compound lifts (squats, deadlifts, overhead press) trains whole groups of muscles at once, including the crucially-important stabilizers which are often neglected in machine-based training.
Starting Strength and Stronglifts are two extremely similar barbell training programs with a very large number of success stories. I've been doing the Stronglifts routine for three months, and am transitioning into Starting Strength as I make my way through the extremely thorough book (which goes into extremely helpful detail about performing the lifts with correct technique). In three months, my squat is now 195lb, deadlifts are 235lb, overhead press at 90lb, bench at 125lb, and barbell rows (which I'm phasing out in favor of power cleans) at 125lb. And I continue to add weight almost every single time I go out.
The numbers aren't super impressive by themselves, but for only three months from having starting at the weight of the empty bar (45lb), I'm seriously thrilled.
I recommend you read this archive of Bill Starr articles: http://billstarrr.blogspot.com/
He taught Rippetoe much of what he knows back in the day. I think Starr articles are way more readable and useful than most of Rippetoe's stuff to be honest.
I've noticed men avoid these classes because tend to be a majority female attendance (at least at my gym). I do feel like the classes are also geared towards women, but that could just be me or my gym (they call is body-design). I'm not intimidated by that, but I feel like many guys are.
I do these with my girlfriend usually, which helped get into it initially, but I'm often the only guy. Doesn't matter, it's a killer workout. Even though I lift, I still do classes like this each week for general fitness.
Be sure to read the FAQ there. The TL;DR version is to pick up one of the two programs mentioned above (5x5 or starting strength).
