Looking at the ranked table, the top half is more split between the two factions but from around rank 7 onwards PHC is indeed far more common. Probably people have come from the campaign and are more familiar with the faction. Also I think people prefer ballistic weapons and can relate to the units more as they are more like current tech than the Substrate. Even when Sub were clearly the more powerful faction, balance wise, the PHC were still more popular, so I don't think that effects faction choice so much.