In pixels, the size of the font to indicate it is not necessary for this, there are points (pt). In all modern browsers, as far as I know, correctly scales any way of setting the pin. To use em you should rather for the sake of a hierarchy of sizes: indoor unit 2em will always have a font size twice the font in an external unit, as if we did not change anything. Plus, you can take into account non-standard font in the user's system.
Pixels are used in the setting of margins and size of elements, but not always. If you want the indent dependent on the font size, it should be set in em. This indentation, for example, is used in the padding of a block quote.