Because I had a lot of trouble with the m/k out of the box with this game (which is an awesome, awesome game btw, once you get a way of controlling flight and combat that suits you) I've tried out a lot of different combinations that I've seen recommended, and I think that while the implementation of joystick emulation that comes as default is actually pretty good, and people who are used to pitch/roll flying will probably find them ok, if you're really used to fps-es and MMOs, probably the best combination, all-round, is this:-
Change the Mouse x-axis to Yaw, use Mouse Wheel for Throttle, have Roll Left/Right on A/D on the keyboard, and have Thrust Up/Down on W/S, with lateral Thrusters on Q/E and forward/back thrusters on SPACE and LCTRL. (Some people might prefer to switch the Q/E and A/D assignments, and/or have Thrust forward/back on other keys). This is one of the more popular combos as far as I can see, and I think it works really well and is intuitive for fps/MMO players.
Also, have whatever key you would normally set to "autorun" in games set to 50% thrust. That way, you default to the "sweet spot", and "pump" forward with forward thrust, and "ease back" withi reverse thrust. (You might think that would be great with W and S as forward/back thrust, and it is, in the sense of being fun for normal flying, but it's actually a "waste" of the W and S keys for combat, as I will explain.)
The key to this is that essentially, to hit things (with Flight Assist ON, FAOFF being another topic) you need to circle strafe (just like in any other game), but because lateral movement is much faster with Roll followed by Pitch, circle strafing is better handled in the vertical direction too, rather than the lateral (though of course you can do it laterally too, it's just a bit more tricky because the flight model is fundamentally Roll/Pitch). And with W and S set to as (effectively) the "circle strafing keys" (analogous to A and D in an fps), it soon becomes second nature with this Roll/Pitch system.
You'd think that having the Roll keys on A/D (or Q/E if you prefer) and pitching with the mose would be odd, but for some reason, it's actually quite intuitive and easy to pitch with the mouse and roll with A/D, the left and right hand work intuitively together for it.
Also, since Roll is actually the fastest movement type in the game, there's no special advantage to having it controlled analogue style (as you do have with Pitch, which is a bit slower). Having it on keys, you roll as fast as you're going to roll anyway, and all you need to do is hold the key for as long as you need to to get in the right position.
So on both counts (rolling and strafing) you have those essential controls on the "handiest" keys (WSAD), right under your fingers at all times. Yaw is "weak" in this game, but it's still essential to fine-tuning aim, and for fps-MMO players, it's pretty intuitive to have as x-axis on the mouse, as you'd normally have it in an fps/MMO.
(Also, another top tip, but for fun, is to have mous 2 assigned to headlook - this makes it feel like you're the avatar in the cockpit and you can look around at any time like you would in an MMO. Great for immersion and instantly checking where something is going as it flys by. You can assign 2nd weapon to Mouse 4 if you do this.)