Thanks to CV Radhakrishnan from tex4ht, the bug has been fixed.
There is an option now to handle the problem with images for math in the align environment. The option is pic-align
htlatex foo.tex "html,pic-align"
Here is the result now using this option
\documentclass[12pt,titlepage]{article}%
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsmath}%
\begin{document}
\begin{eqnarray*}
v^{2} & =& \left( \dot{x}+v_{x}\right) ^{2}+v_{y}^{2}\\
& =& \dot{x}^{2}+l^{2}\dot{\theta}^{2}+2\dot{x}l\dot{\theta}\cos\theta
\end{eqnarray*}
\begin{align*}
v^{2} & =\left( \dot{x}+v_{x}\right) ^{2}+v_{y}^{2}\\
& =\dot{x}^{2}+l^{2}\dot{\theta}^{2}+2\dot{x}l\dot{\theta}\cos\theta
\end{align*}
\end{document}
Here is the output from htlatex foo.tex "html,pic-align"

We can see that align now works fine in htlatex !
Just for completion, if someone is using htlatex, you'd need to also add these 2 lines to your config file to force some of the inlined math to be bit mapped. An example myconfig.cfg
\Preamble{html}
\begin{document}
\Configure{$}{\PicMath}{\EndPicMath}{}
\Configure{PicMath}{}{}{}{ class="math" align="absmiddle"}
\EndPreamble
and now the command is:
htlatex foo.tex "myconfig.cfg,html,pic-align"
eqnarrayis deprecated and should not be used any more as it produces inconsistent spacing. If you still want to do it (I'm not familiar with htlatex), you will need to take care of the special issues of starred and no starred form and probably use\NewEnvironfrom theenvironpackage. Also you should put your actual question into the body and reduce the title. – canaaerus Feb 11 at 6:26\renewenvironment{align*}{\begin{eqnarray*}}{\end{eqnarray*}}if you keep all the above warnings in mind. And you must promise never to use it withpdflatex.:-)– T. Verron Feb 11 at 6:55\begin{document}, put your redefinition statement after\begin{document}. – deimi Feb 11 at 7:30