Why are there only two women in "Julius Caesar"? Where is King Lear's wife? Where is Leonato's wife in "Much Ado About Nothing"? How many plays can you name with all female cast? (Thought not).
Remember drama started as an activity only carried out by men, in Greek times, but also in Elizabethan and Restoration times: it was only relatively recently that women were allowed on stage. The culture of drama, then, has always favoured actors rather than actresses: feminist critics might argue that it has something to do with a patriarchal bias in society, but for me, it's simply a habit that writers are still getting out of.
That said, maybe Beckett just wanted an all-male cast so that the post-apocalyptic world of "Waiting for Godot" had absolutely no hopes of regeneration or producing children. Who knows?