Why did Silver choose Idiot Hero John Reid instead of his Ace brother, Danny? Look at what John got from being chosen by Silver; Improbable Aiming Skills and a vaguely-defined and inherently unprovable "inability to die in battle". Dan was already a badass Gunslinger, meaning Silver couldn't have been of much help to him. John, on the other hand, was an incurable idealist who lacked only the power to live up to his ideals - perfect to become the Lone Ranger.
Tonto says that, like the Wendigo, Butch Cavendish has the power to throw nature out of balance. During this conversation, Tonto throws a roasted rabbit to the other rabbits, causing them to go into a carnivorous frenzy. This may foreshadow Tonto's past and how he had a hand in "throwing nature out of balance". The rabbits act like a metaphor for Cole and Cavendish, and how Tonto leading them to silver made them greedy and heartless.
While the silver bullet wasn't used in killing Tonto's perceived Wendigo, the metal still killed the last man he declared as one by crushing him to death.
Why was Latham Cole so intent on shortening the railroad and building across Comanche territory? Historically, taking the longer route around it would have enabled him to squeeze more money in land grants from the US government.
While Cole truly did believe in the railroad, it was also partly a cover for the silver plan, which would have netted him more than the land grants ever would have.
If Cole and Cavendish didn't want anybody else to know the silver's location, why did they leave Tonto alive? Especially when you consider that:
There had to have been other children in that Comanche village they slaughtered
It would be an easy way for them to get their watch back
Arrogance probably. He's just a kid. Who would believe him? Plus, what were the chances of him actually surviving alone? The plan works as Tonto goes completely insane without them lifting a finger and he would have failed to get revenge if not for John. They probably just gave up when they didn't see him in the village. Plus, sadism.