Consider the lifestyle of pre-modern dogs and humans. Pre-modern dogs (wolves) worked as a pack, and had a territory in which they hunted and lived. Many of their prey animals (deer, for example) could swim, so they needed to be able to swim to catch some prey. Swimming could also be useful for wolves to travel to other territories, or to follow migrating prey species.
Humans on the other hand, more commonly relied on tools and knowledge to hunt. Technology such as boats, rafts, or canoes could be used to travel over water. Hunters could lead prey animals into traps and away from water. Additionally, humans did not have protective fur like wolves did, so getting wet could be more hazardous (hypothermia).
So, it stands to reason that dogs have had more of a past need for swimming instincts, where humans have had less of a need.
Just a thought, I could be way off.