Either will get you in shape...
I took a quick look at these lines on Trek's site. Both would fit my definition of being "hybrid" bikes in that they fall somewhere between Mountain bikes and road bikes. The "FX" line leans a little more toward road design, with narrower tires, no suspension, slightly lower handelbars in relation to the seat.
The one that will give you the best exercise is the one you ride the most, so it really comes down to comfort and where you plan to ride. If you are going to be on paved roads and bike paths, and the FX is comfortable for you, it probably is a little more efficient for longer rides. But if you feel more comfortable with the wider tires, front suspension, etc., and/or plan to ride more dirt roads or unpaved bike paths, maybe the hybrid is the way to go. Try to test ride both and see what you think.