Travelers along the Oregon Trail in the 1840s were very likely to meet Native Americans in incidental encounters. Natives frequently used sections of the Oregon Trail as they provided useful routes between places they occasioned. The native people often would want to trade, and many would have been just curious. The westward travelers in the 1840s would have encountered natives that tended to congregate around forts like Fort Kearny, Nebraska, Fort Laramie, Wyoming or Forts Hall and Boise, Idaho because, at this time, these were trading hubs that had been utilized by natives, fur trappers and explorers for several years.

West of the continental divide, travelers traded for food with natives in the Snake River and Umatilla Valley regions. This is documented in the early 1850s, but likely preceded that period.

Many of the early Oregon Trail users were guided by famous mountain men such as Thomas Fitzpatrick or William Sublette. These guides were eminently familiar with dealing with native groups and individuals along the route and would have been able to manage the encounters appropriately.

If you are limiting your question to just the 1840s, adverse encounters with natives would have been very rare. I can find no evidence of adverse encounters resulting in deaths until around 1845, and even after that, the threat of Native American attacks paled in comparison to accidents or disease. When traveling in the 1840s, you were far more likely to be seriously injured by a mule kick or contract cholera than to be attacked by Indians.

Dary, David. The Oregon Trail. New York: Knopf, 2005.

Oregon Trail-Oregon Encyclopedia

Leroy R. Hafen. Broken Hand: The Life of Thomas Fitzpatrick, Mountain Man, Guide and Indian Agent. Lincoln: UNP, 1981.