How do you maneuver the ship when you turn flight assist off? The throttle seems to have no effect, and lateral movement seems only to work in the side to side and rear directions. Thanks.

Trying to remember since I haven't played for a while but try WASD, as those are the thruster override commands. That's assuming you're talking about I-War 2.

If you don't have it already, here is the reference card for I-War 2: http://www.gog.com/forum/independence_war_series/reference_card/post16

Yeah, I already have a reference card. In fact, I made one myself here:

http://isometricland.net/keyboard/keyboardchart.php?gam=25&sty=1&lay=1&eff=

[edit]

Problem was a control binding mistake I made. Fixed now.

Well, with fly assist off, you just fly forward with constant speed, due to inertia (as in Newton's First Law of Motion), so you actually can't change velocity or direction of flight.

Then, why would you do that?
The idea is, you can aim your ship beside some capital ship for example (that is, a bit left or right off the enemy ship), get some speed, then glide on that trajectory in "unassisted flight", while you turn your ship's nose (and its cannons) toward the target and shoot it as you fly-by.

This worked well in first I-war and its expansion, which didn't have dedicated strafing keys. But in EoC I found it much more effective to use [A] and [D] keys for side movement and strafing around the slower ships, while pounding them. If you combine strafing with a bit of roll movement (by turning the joystick around its vertical axis), your strafing will become a sort of spiral movement, which makes it very difficult for enemies to hit you.

So there's not much point to use unassisted flight in EoC at all. Except perhaps if you you're running away and don't want to lose your forward momentum while turning your ship around and shoot at your pursuer, while flying backwards.
In this case just press ALT, while you're turning the ship around and reversing the engine thrust, then release it when you're facing the enemies (and flying backwards).