I see what you mean in a way - that the male stick figures don't have long hair. Again, though, this is only your viewpoint - very rarely is the stick figure's gender actually mentioned in the text of the comic or otherwise. Besides, not all females have long hair, many of the not-overtly-female stick figures may also be female despite not having long hair. Only your viewpoint, again.
The internet: where you can argue about the gender of stick figures.
Secondly, long hair denoting femaleness is a cartoon trope and that's how it's used in xkcd (note my issue is not the trope itself here, but that it is used by someone who says they're passionate about equality). Using your argument, you could argue that the cartoon characters with long eyelashes and pink bows in their hair could be male, but of course in real terms that's never how they're seen.
This is part of the 'othering' of women - "you look different to what 'normal' looks like".
In any case, common male hairstyles in anglo societies still stand out from the head, as much as the non-dangling part of ponytails.