Transit is a noun and refers to the movement or passage itself. So an example might be - "The transit of Venus across the Sun is a very rare event."
It is countable - "There have been only two other such transits recorded."
Transit is often used with "in" - "The goods are in transit at present."
Transport can be a noun or a verb. As a noun it refers to a system or means of transport. So it refers to buses, ships, etc.
As a verb transport means "take to a different place". So - "The goods were transported by sea."