hum well you can change your base color when tweaking your race at the beginning of a new game, other than that ... I don't know
but there's also a few things you can try before changing those colors...
first and foremost depending on you specific screen and graphic card and settings, the actual color shown can differ by quite a bit
For example, if you use AA (antialiasing located ni video options) and if you have an Nvidia graphic card, you have to know that by default, Nvidia doesn't correct the gamma of its Antialiasing (this can be corrected though) so that's a first thing...
Your screen may not be well adjusted for colors too, most screens are setup by constructors so that you think colors on that screen are better, despite the fact that they are not accurate and often too much blue, too much green and/or too much red...
Also If the nebulae option is turned all the way to the max, the background color of the nebulae may make things more difficult to see. No nebulae is better in this case...
I'm just hinting at things here and there just so you know, but in any case it's true that terran autopilot lines don't really stand out, so maybe just changing their colors to brighter ones will do the trick for you...
