Some suggestions that I haven't really seen other people bring up...
Large, territorial megafauna
Humans are kind of lucky in that most of the extant marine megafauna aren't huge, and of those that are the majority are non-aggressive filter feeders. Of the large predators that do inhabit the oceans and pose a threat to ships, orcas are weird in that they seem to deliberately avoid antagonizing humans, whereas great white sharks can sink small canoes but cannot harm larger ships.
Sperm whales are about the only large ocean animals that are known to attack ships. They don't deliberately do so, but they have been known to sink ships several times their size if wounded by whalers or if they believe the ships to be intruding on their territory during the mating season. An ocean filled with larger predatory marine life that can either view a ship as prey or is highly territorial and has some mechanism that can deal damage to a ship (like the sperm whale's spermaceti-filled battering ram melon) would make sailing much more hazardous because now there is ocean life that can stop a voyage in its tracks.
If ocean life is aggressive enough it may even slow usage of smaller boats like canoes, if moderately large predators are attacking and sinking small craft every time they get in the ocean. As a result, even if larger ships would be save humanity might never take the necessary intermediate steps to get there.
Some species may choose to travel to certain locations to breed or raise young at certain points of the year, much like whales and great white sharks do today and megalodon is thought to have done so in the ancient past. If sufficiently territorial, this would make some islands virtually impossible to travel to for some periods of the year, lest the ships be sunk by angry males believing the ships to be challenging them or females protecting their young. This would force these islands to be highly self-sufficient or starve given they would be frequently cut off.
Extreme tides, which would have to be caused by some kind of shift in Earth's rotation or Earth's relationship with the moon, could potentially make sea travel extremely hazardous. What this would do is cause large areas of the coastline to be underwater at high tide, but exposed at low tide. This would result in boats very easily becoming stranded at low tide if they anchored too close to the island, or potentially wash rowboats out to sea if people are not very, very careful where they anchor them and drag them far above the high tide line.
Another consequence is it would make navigating nautical hazards very unpredictable and unreliable. An outlet that may be perfectly navigable at high tide could be filled with dangerous reefs that would pierce a hull at lower tides. What areas could and could not safely hold a boat would be extremely variable and depend on detailed knowledge of local topography.
Rarity of Fresh Water
Abundance of fresh water typically makes or breaks human habitation of islands. Of the few islands that were not successfully colonized by pre-industrial/age of sail humanity, most of them, such as Aldabra or the Galapagos Islands, lacked any permanent sources of fresh water, meaning they relied on imports of water from elsewhere to be habitable and could not be permanently settled without being supplied water externally. In a world where most of the landmasses are flooded, it stands to reason that there would be a lot of areas that lack fresh water due to the small size of most landmasses. This would mean that ships would have to bring all their water with them or risk death by thirst, making travel in these areas extremely expensive.
Most islands without fresh water do have large tortoises that could be used as food, but this is mostly because they lack fresh water and therefore humans. Tortoises are known from most large oceanic islands but the ones that had fresh water on them were all wiped out shortly after human arrival (e.g., Madagascar, the Mascarenes, the Bahamas, Bermuda, the Antilles, the Canary Islands, etc.)
Other users have already mentioned this, but I would add in a world with few major landmasses, there would be no continents to disrupt the flow of ocean currents and as a result crossing the equator would be very difficult. The doldrums would stretch virtually unimpeded around the globe and there would be very few ways around them. Few currents would travel through this zone because there would be no trans-equatorial continents, and people would be unable to hug the coastline or travel on foot across the continents to avoid them.
It may be harder to monopolize sea travel than you think
It's amazing to think how far humans are able to get with so little technology. Humans were able to disperse from Indonesia to Australia/New Guinea over water 50,000 years ago, with otherwise Stone Age technology. Furthermore, the Polynesians were able to disperse to nearly every island in the South Pacific based on a somewhat limited tech base. Polynesian sailing was very refined and the Polynesians had a complex knowledge of shipbuilding (using designs like outrigger canoes) and navigation, but the Polynesians made their actual boats without the use of metallurgy or heavy industry (which if anything only makes the feat more impressive).
What this goes to show is that with enough time and motivation even Stone Age peoples would likely learn to be able to navigate the ocean, especially if the world was a series of islands and ocean travel was critical for survival. If people didn't learn to sail it would make them incredibly vulnerable to being wiped out if a volcano erupted, the environment was depleted through hunting or deforestation, or if the environment became too heavily degraded for farming or fishing the local waters. Even if the seas were hard to navigate people would try anyway.