Because each coastal territory you take is one less your trading territories earn, choose your trade base carefully. Also, once you have that base, expand inland and into useless coastal territory as well. Try to slowly build up fleets, once you get two or more shipwrights running, things will come along nicely. I try to get a minimum of 2 ships and 3 ships per foreign ship in a sea tile, for storms/combat etc.

Here are the trade bases I usually use based on faction:

Middle East - Egypt, Antioch, Tripoli, and that other coastal one.
Besides a one territory defence from Africa and a threat of an Anatolian invasion, this is pretty secure. Even when fleets only reach around to Italy, you are still pulling very good bank. Crete and Cyprus usually have ports even though they have nothing to trade, meaning you get two easy provinces to sell to.
A suprising number of factions can try and claim this bread basket. The Spanish, Italians, or Hungarians are in decent positions to try and spam crusades for the region. The Egyptains already have a decent position and the Almohads are usually busy with the Spanish. Byzantium has a good shot at the region. Of course any Turkish Sultan must secure these blessings if he hopes to survive at all.

Northwestern Europe - Wessex, Northumbria and Flanders all are worth owning, especially if you are the English and French.

Venice - Highly contested area open to Byzantines, Italians, Papacy, HRE, France, Hungarians.