Yes, there are some downsides to using a simulator to learn how to land a plane. However, there are significant benefits to landing in a simulator over real-life.
This is the big obvious advantage. Learning to land in the sim costs basically nothing compared to landing in real life which usually costs around $10 per attempt when renting a plane.
Practicing landings in real life allows for one trip around the pattern every 5 minutes or so. This means that in a 1 hour lesson you usually can’t do more than 12 landing attempts.
The simulator however, let’s you save and load quickly. A good approach leads to a good landing so make sure to spend plenty of time practicing both. It is nice to save on midfield downwind at pattern altitude and the correct speed and then reload this save over and over again to quickly practice approaches to landing.
Once you get the approaches down try saving about 100 feet before the end of the runway so you can practice the touchdown over and over again. Some simulators will even allow you to load your save with a joystick button so you can land again and again!
When landing a real plane you can only access one view: the 3D cockpit view. This is nice but the simulator allows you to land from chase view and really get an idea of how the airplane is behaving during landing.
Practice landings in the chase view sometimes and you will get better at touching down softly.
Debriefing after a flight is one of the best ways to solidify your learning. Use replays of your landings to help recall what worked and what went wrong.