In addition to what Bob said the main problem is really in **renderer** of your maths.

MathTran does not support colours at all

Mimetex does support those few colours that Bob mentioned (moodle is using this if no other option is available in tex filter)

Most distributions of Latex (TexLive, MikTex,...) do support color if you have added to Tex filter settings and LaTeX preamble

\usepackage[usenames]{color}

Default LaTeX preamble does not support colours.

MathTex supports 68 standard color names known to dvips and colors like #XXXXXX

Finally MathJax supports all colors and you can use either \color{...}{...} for any parts of mathematical notations or add colors to html elements (for example spans) around mathematical notations (for example with editor color tools) and mathJax takes the colors from surrounding element. MathJax supports also scaling http://www.mathjax.org/demos/scaling-math/ that makes it much more flexible renderer that image based latex renderers. All you need to do to use mathJax with moodle 1.9 is to add the necessary script tags for example to your theme header.html or meta.php - or upgrade to moodle 2 that has a couple of other tools available