That's probably because MathML support is pretty poor in most browsers and even on Firefox, which has the best support, it isn't really good enough for all uses. MathJax has various backends to render LaTeX formulas, including SVG, MathML and HTML-CSS. Here's what the MathJax documentation says about the MathML backend:
"The NativeMML output processor uses the browser’s internal MathML support (if any) to render the mathematics. Currently, Firefox has native support for MathML, and IE has the MathPlayer plugin for rendering MathML. Safari has some support for MathML since version 5.1, but the quality is not as high as either Firefox’s implementation or IE with MathPlayer. Chrome, Konqueror, and most other browsers don’t support MathML natively, but this may change in the future, since MathML is part of the HTML5 specification."
"The advantage of the NativeMML output processor is its speed, since native MathML support is usually faster than converting to HTML-with-CSS and SVG. The disadvantage is that you are dependent on the browser’s MathML implementation for your rendering, and these vary in quality of output and completeness of implementation. MathJax relies on features that are not available in some renderers (for example, Firefox’s MathML support does not implement the features needed for labeled equations). While MathJax’s NativeMML output processor works around various limitations of Firefox/Gecko and Safari/WebKit, the results using the NativeMML output processor may have spacing, font, or other rendering problems that are outside of MathJax’s control."
"The NativeMML output processor uses the browser’s internal MathML support (if any) to render the mathematics. Currently, Firefox has native support for MathML, and IE has the MathPlayer plugin for rendering MathML. Safari has some support for MathML since version 5.1, but the quality is not as high as either Firefox’s implementation or IE with MathPlayer. Chrome, Konqueror, and most other browsers don’t support MathML natively, but this may change in the future, since MathML is part of the HTML5 specification."
"The advantage of the NativeMML output processor is its speed, since native MathML support is usually faster than converting to HTML-with-CSS and SVG. The disadvantage is that you are dependent on the browser’s MathML implementation for your rendering, and these vary in quality of output and completeness of implementation. MathJax relies on features that are not available in some renderers (for example, Firefox’s MathML support does not implement the features needed for labeled equations). While MathJax’s NativeMML output processor works around various limitations of Firefox/Gecko and Safari/WebKit, the results using the NativeMML output processor may have spacing, font, or other rendering problems that are outside of MathJax’s control."