I think you misunderstood the message. It is saying that if you turn off the hardware acceleration don't expect FS2002 to run very well. You definitely want hardware acceleration turned on in other words.
With the little hardware acceleration box checked, Flight Sim is able to use all the bells and whistles on your graphics card. With it unchecked, your graphics card will be just going through the motions, your processor will have to do all the work, and the game will be apalling.