Why did people stop using the Oregon and Santa Fe Trails?

The Santa Fe Trail was heavily used during the Mexican War because of the large volume of military supplies that were transported from the Missouri River Towns to the Southwest. 1860s Santa Fe Trail was shortened at its eastern end, and with the coming of the Santa Fe Railroad, the trail was virtually deserted.

The answer to the question above is the federal system of government.
A system of government in which power is divided between a central authority and constitutional political subunits is called the federal system. This type of government system combines the central government with regional governments to form a single political system.