Our kids naturally broke themselves of wanting to be swaddled. Our son loved it, our daughter never really wanted to be.
Have you tried putting her in her swing, bouncy seat, etc. to take her naps during the day? That was the trick for us with both kids. They preferred that enclosed kind of environment and the motion.
The car was always a good thing for us - I'm convinced it's because I likely drove 30,000 miles during each pregnancy, and they liked the sound of the car's engine.
Just remember that at 3 months, your baby still completely runs on instinct. She doesn't know that she should be doing things differently and is simply communicating in the only way she knows how to tell you what she needs is different than what she's getting.
Good luck! The next few months are SO much fun!