If it goes away in neutral, you're fine. All engines tend to feel like they're running rough at idle and under load. That is the point where the engine is putting out its least power and it is straining against the brakes that are keeping the vehicle from moving. When you take the load off it by shifting to neutral it returns to a normal idle. Similarly, if you take your foot off the brake and give it more gas the engine puts out more power and moves you forward -- now the engine is doing what it wants to do.
Some of the early Patriots had poorly adjusted hoods and they tended to jiggle when idling in gear which only exacerbated the perception.
PS. welcome to the site!