By building a good, solid coop and run. Luckily coyotes are big and thus not hard to keep out. But, unless you could eliminate all of them, you won't be able to keep them away altogether. Assume they are going to show up every night, in choosing the ways to construct your run and coop. Coyotes are not dumb animals.
The lower portions of the run should be heavy gauge wire of sorts, with strong framing to support it all. 3 or 4 feet high, with an underground skirt. Its a bit of work, but do it right to begin with, get it over with. The higher the better. 1 layer of chicken wire isn't going to keep them out (nor other predators). Cage wire, or garden fencing, somethng heavy. Watch places like craigs list for used sections of fencing, chain link, etc.