The belief of thoughtful Palestinians and of Americans living there such as the personnel of the Friends Schools in Ramallah is that the check points are designed to put as much pressure as possible on Palestinians without provoking mass open rebellion. The intent is to humiliate and to change lifestyles, for example to make people decide it isn't worth going to the doctor they like in Jerusalem, but go to a Ramallah doctor instead.
Since the Israelis really wish the Palestinians would disappear (and Labor is simply more polite about that goal than Likud is), this continual discouragement hopes to drive them abroad. The harassment of sympathetic foreigners is probably intended to keep us from coming back. I know that if I have reason to go back, I will investigate traveling through Jordan (the same airlines fly there).
To get a feeling for the pettiness of it all, read about Tania and Charlie's wedding