Why are my ships on negative profits, uhuuhu

All port prices are not the same : each has a different selling or buying price for a product. This price can also change depending on supply and demand. For example : currently Tools cost 24g in Chalkos and 18gc in Newland. Buy in Chalkos to sell in Newland and you lose 6gc per unit. Buy in Newland to sell in Chalkos and you make 6gc per unit.

So, it is likely you are buying from a port with a higher price than the port you are selling at.
The other way this happens is if you are storing supplies on one leg of your trade route and the cost of those supplies exceeds the profit made on the other legs of the route.

So. Examine your trade routes carefully to make sure you can turn a profit on each leg as well as overall if you store any. Look to make a profit on both journeys to and from a port. You can select up to four ports on your trade route so with clever planning you can look to gaining the maximum profit on each leg: Port A > B > C > D then back to port A again.