Traveling by sea might have been really dangerous - not more than traveling by land in certain areas - mostly because of living hazards.
Crews that do not pay homage and make sacrifices to Umberlee, or that are not protected by Valkur or Shaundakul, might be ambushed by creatures of the deep, and the same goes for enemies of the Society of the Kraken.
Some regions are also controlled by the typical D&D sea civilizations, including kuo-toa and sahuagins, and pirates are surely a thing, but land travel has orcs, goblins, kobolds, the more rural giants (ogres, trolls and hill giants) and bandits of all sorts. The only reason why traveling by sea might be more dengerous is that the ships are mostly used by land-dwellers and their guards are not really good at patrolling the sea as they do with the high roads. While this is also true for the real world, the real world balances that by having the main source of piracy among land-dwellers as well. D&D has underwater races that are way more accustomed to the environment. Basically, ships have the same protection as conestoga caravans crossing the wild west. There are hostile Indians, there are pacific Indians who won't go out of their business to protect them and there is the rare fort here and there (guard ships): I'd expect ships to travel in groups and with armed escort. Especially convoys who want to travel to the hostile, unknown coasts of Matzica to look for the riches Amn is importing already.
Coastal travel is way safer because there are civilized cities on the coast and partolling the coast would be expected.
Ships from large merchantile companies are expected to board some kind of priest of mage that who cast control weather or generate winds on command, making weather a minor inconvenience.
The spells and equipment published in It's wet outs- uh, I mean Stormwrack make the whole seafaring thing safer. Sextants do exista and they "only" cost 250 gp (and even without one, using stars to find the north is just a survival check). Control currents, favorable wind and the everfull sails make it hard to be hampered by a calm, while detect ships and flowsight protect from being approached by pirates and sea creatures.
Casting locate city from Races of Destiny means being able to find nearby ports. As always, casters are really great at helping even outside of combat.
Of course, adventurers more easily sail towards the danger than not, but I'm pretty sure crews might hire adventurers to protect their charge. How many adventurers are ok with this kind of life depends, I guess, on how much they get paid.