When you're new to lifting, it's understandable to find comfort in stationary weight machines; there's already a basic set-up, which takes the guesswork out of the movement. Stationary machines might give you the edge to move more weight initially, but it's important to realize that they work on a fixed axis that only allows you to move in one or two planes. Sure, you'll still gain strength, but the functional fitness gains will be minimal.
Free weights, on the other hand, allow you to move forward, backwards, horizontally and vertically—strengthening patterns of movement you use in everyday life. Instead of opting for one or the other, try using a mix of both. Try kicking off your workout with free-weight compound movements like the squat, bench press or deadlift. From there, use a few machines to hone in on developing specific muscles.