how do the capsule and flagella contribute to the pathogenecity of microorganisms?

Answer 1

Capsules act as a protective coating, protection form the body's immune system. Flagella allow motility and some types of flagella allow MO's to attach to the host body, thereby allowing it to evade the host immune system.

Answer 2

Capsules help the microorganism to hide out until conditions improve. The flagella lets it move around. Both of these make life better for the microorganism, giving it more opportunity to infect.