They back up their work with a workmanship warranty.
Not all contractors can offer manufacturer warranties that include coverage of the contractor’s workmanship. If a contractor installs the roof incorrectly, it may take months or years for the damage to show up—and insurance won’t pay for it. If the contractor won't fix their mistake, your stuck with the bill. When researching a company make sure they warranty their work.
They have the proper licensing, bonds and insurance.
If your gonna hire a contractor, make sure they have all the proper licenses and insurance. Inproper insurance could lead to litigations between yourself the homeowner, and the contractor. There is a reason you may have heard of someone getting a brand new roof for seven thousand dollars; the roofer likely was not insured, not licensed and did shoddy work not up to local codes. Always make sure that the contractor provides you with copies of insurance and licenses.
Pay your deductible.
There is no shortage of companies out their who claim they can repair or replace your roof without the homeowner having to pay out of pocket. In any claim work done through your insurance the property owner is always responsible for paying their deductible. Any company who pays that on your behalf is committing insurance fraud and endangering you the property owner.
It's your property so you should get to decide on the new materials used right? Correct. The style and color of shingles being installed should always be decided by yourself. If you qualify for a complete roof replacement and the insurance company is paying for it, it may be worthwile to look at any upgrades you can decide to pay out of pocket, for example:
You have a 3 tab roof now and want to upgrade to the same dimensional shingles like your neighbor. It is a stronger roof and increases property value, why shouldn't you get the option for an upgrade?