The iPad (and iPhone/iTouch) usually use MathJax's image font mode,
which means that images of the characters are used. These can't be
recolored, and so the \color command will not affect them; that
requires actual. fonts. The more recent releases of iOS have support
for web-based fonts, but it has been buggy and not really very
reliable. I haven't had the chance to test the most recent release,
so perhaps that will be better. If it turns out to be, then MathJax
can take advantage of the web-based fonts (as it can for most other
browsers), and that will make \color effective for the iPad.
Davide