Why is transit in goods free but trade is not?

In my previous two posts on the value of the WTO, I argued that when governments set trade policies independently, they focus on domestic effects but often overlook the costs imposed on trading partners. International trade agreements help governments take account of these cross-border spillovers (terms-of-trade externalities) by encouraging reciprocal negotiations over trade policy. While these negotiations will reduce trade protection, they will not necessarily lead to free trade. But if governments do not generally commit themselves to free trade, why has freedom of transit for goods been seen differently?