All other browsers (not IE6) scale the size of the entire layout in px. So what is the purpose of using em and% if we are not thinking about IE6?
Have you considered all the major mobile devices (e.g. phones)?
If you specify the font size em, your codes will be more flexible and easier to maintain, if you want to subsequently change the font size. Also, as Dan McG said, not all browsers scale in pixels.
em % help
Even if all browsers support scaling of the entire layout as you describe, the user interface is not optimal if it should scale the web page every time to match their resolution.