Question

If ther are protons inside an atom why alpha particles are deflected

Answer 1

Protons and Neutrons are concentrated in the middle of the nucleus existing as 'nucleons'. It is important to know that Alpha particles are doubly charged helium atoms, I. E. They are positively charged. As per Rutherfords experiment, most of the rays went through undeflected, this is due to the nucleus occupying such small area. Few rays underwent deflection as they went close to the nucleus and the positive-positive repulsion caused it to deflect.