Hey, you know what? I sympathize. I play FS2 on an XBox controller pretty much always. You still have to reach out to the keyboard now and again, but you can get your main controls onto the 360 controller. I use it because I feel that in space combat, one joystick just doesn't cut it. You can move in too many different directions. I make use of both joysticks and the hat stick to control movement.
You need a couple of programs. I'm going off the assumption that you're using Windows XP or later--this will probably work for other OS's, but I don't know for sure.
First, you need PPJoy. (Google this one. There are a lot of versions and lot of places to get it.) Once you download and install this program, set up a virtual joystick. (The included documentation is very straight-forward and will lead you through this.)
Next, you need GlovePIE. You can find it here: http://glovepie.org/
Once you have GlovePIE set up, you can use its emulation and the virtual joystick you created with PPJoy to control map your Xbox controller to pretty much any darn thing you want, and FS2 does support the extra joystick axes to a limited extent. Admittedly there are still some limitations, but I find that this setup gives me all the basic functionality I need.
PM me if you run into any problems with getting this stuff set up (although I don't think you will) and I'll be glad to share whatever small body of experience I can!
For reference, here's the PIE setup that I use, with the comments I left myself. Again, configuring GlovePIE this way assumes that you have Windows and the accompanying drivers for the XBox 360 controller. Otherwise, your 360 controller input may be called something other than "XInput."
//for Xbox 360 Controller, FS2
//This ties the PPJoy sticks to the left stick, right stick, and triggers
PPJoy1.Analog0 = XInput1.Joy1X
PPjoy1.Analog1 = -XInput1.Joy1X
PPjoy1.Analog2 = XInput1.Joy2X
PPJoy1.Analog3 = XInput1.RightTrigger
PPJoy1.Analog3 = -XInput1.LeftTrigger
PPJoy1.Digital0 = xinput1.A
PPJoy1.Digital1 = xinput1.B
PPJoy1.Digital2 = xinput1.X
PPJoy1.Digital3 = xinput1.Y
PPJoy1.Digital4 = xinput1.LeftShoulder
PPJoy1.Digital5 = xinput1.RightShoulder
PPJoy1.Digital6 = xinput1.Start
PPJoy1.Digital7 = xinput1.Back
PPJoy1.Digital8 = xinput1.LeftThumb
PPJoy1.Digital9 = xinput1.RightThumb
PPJoy1.Digital10 = xinput1.Up
PPJoy1.Digital11 = xinput1.Left
PPJoy1.Digital12 = xinput1.Right
PPJoy1.Digital13 = xinput1.Down
I tinker with the layout a lot, but at present my controls are mapped thus:
Left stick: Pitch and yaw
Left stick press: Toggle glide
Right stick: Roll (just roll, nothing on Y axis)
Right stick press: Toggle auto-match speed
D-pad or hat stick: Thrust up, down, left or right
Right bumper: fire primary
Left bumper: fire secondary
Triggers: relative throttle control
A: Target in HUD
B: Target next nearest enemy
Start: Cycle next target
Back: Cycle previous target
As you can see, I've left most of the technical fiddling--such as energy and shield adjustments--on the keyboard.
And if you like this method and you get it all set up, let me know what control schemes you come up with!