While it is true that the fur/hides of the bison and the animal as source of food (the
railroad, for example, found it a convenient means for feeding workers) was a factor, the decimation of the North American bison also had a darker motive. It was part of the attempt to deal with the "Indian problem."
Many of the plains Indians were inextricably linked to the bison as their chief source of subsistance (also using the hides as well as for food). The army and the government were well aware of this, so encouraging the slaughter of the animals went in line with attempts to remove the Indian from the picture. How and its consequences of were of less importance than the result. So it didn't matter whether it was through actually fighting (or the murder of innocents: see Sand Creek Massacre, where nearly 200 people were killed and in many cases mutilated, of which the majority were women, children, the infirm, and the elderly, all under a white and American flag), sickness and starvation, or all of the above forcing them into moving to reservation land and away from land desired by the government and settlers.
"The civilization of the Indian is impossible while the buffalo remains upon the plains. I would not seriously regret the total disappearance of the buffalo from our western prairies, in its effect upon the Indians, regarding it as a means of hastening their sense of dependence upon the products of the soil and their own labors."
Interior Secretary Columbus Delano, 1873
General Philip Sheridan, who was in charge of the army that was "dealing" with the Indians of the plains, strongly supported the killing of the bison (as well as unconditional warfare against the indigenous peoples). Once he was asked by some "concerned Texans" about what could be done in order to end the hunters' slaughter of the bison. He replied "let them kill, skin, and sell until the buffalo is exterminated, as it is the only way to bring lasting peace and allow civilization to advance." When legislation was introduced into Congress (eventually vetoed) in an attempt to save the populations of the animal by letting no one but Indians kill "cow buffalo," Sheridan opposed it, suggesting they should "strike a medal, with a dead buffalo pictured on one side and a discouraged Indian on the other" to present to the "buffalo hunters."
Though the bill passed both houses of Congress, it was also greatly opposed and for the reasons one might suspect:
"There is no law that Congress can pass that will prevent the buffalo from disappearing before the march of civilization. They eat the grass. They trample upon the plains upon which our settlers desire to herd their cattle. They destroy the pasture. They are as uncivilized as the Indian."
"The solution of the Indian problem is to confine these Indians upon as small a tract of land as possible, and make it a necessity for them to learn to labor and to get a sustenance from the soil as the white man does."
"It would he a great step forward in the civilization of the Indians if there was not a buffalo in existence."
(the three above quotes from an article from the November-December 2000 Earth First! found online)
The two prong attack (on the Indians, themselves, and on their means of subsistance) worked extraordinarily well. By 1889, only 835 bison remained. By the end of the century, few non-reservation Indians remained.
(Sources: Ward Churchill's excellent 1997 A Little Matter of Genocide, www.britannica.com, and the pages on the documentary "The West" at www.pbs.org; Sheridan quote from Dee Brown's Bury My Heart at Wounded Knee 1970)