Even if there wasn't a difference between electron and proton mass, it would still provide net force if the craft is already moving relative to the background plasma (I.e. swimming upstream). Incoming electrons from the front get reflected at their original velocity, but protons get accelerated out the back at arbitrarily high speed (limited by the electric field). The massive difference in electron and proton means it can provide force even if the plasma is coming from behind, which is much more useful.