As long as you cook the chicken to a high enough temperature which means you cook the chicken properly and all the way through then the salmonella should be killed in the process of cooking it.
It doesn't guarantee that you won't get sick from Salmonella but as long as you handle the chicken properly and make sure it's well done and fully cooked then you shouldn't get sick with Salmonella Poisoning.
Many other meats such as hamburger, pork as well as other foods such as eggs, vegetables and fruits can even contain Salmonella.
The cooking usually causes the Salmonella to fully die off though because the Salmonella cannot usually survive the cooking temperatures as long as you cook the chicken all the way through.