Each cell within the align environment forms a group, localizing the extent of the colour change. If you wrap the colour change around the outside of align, it spans across the internal cells:

\documentclass{article}
\usepackage{xcolor,amsmath}% http://ctan.org/pkg/{xcolor,amsmath}
\begin{document}
{\color{red}\begin{align}
x &= 1\\
y &= 2
\end{align}}
\end{document}
You'll notice that this sets even the equation numbers in \color{red}. This is easily fixed by adding the following to your preamble:
\usepackage{etoolbox}% http://ctan.org/pkg/etoolbox
\makeatletter
\patchcmd{\math@cr@@@align}% <cmd>
{\place@tag}% <search>
{\bgroup\color{black}\place@tag\egroup}% <replace>
{}{}% <success><failure>
\makeatother
The above etoolbox-patch inserts a black colour-change around the number-printing mechanism \place@tag:

For individual colour modifications to each cell/component of the line, insert \color{<colour>} in the respective cells you want to use colour <colour>.