The fatal flaw in Rutherford's model is that it contains charges that are accelerating. The charges are on the electrons and the acceleration is due to the electrons always changing direction as they move around their orbits. Therfore the electrons are not accelerating they are merely in an non-symmetic orbit around the nucleus.
Rutherford said that electrons are arranged in orbits around the nucleus, but the electrons are really scattered in ORBITALS
There's nothing wrong with his model, it is just that, he didn't find out that electrons are revolving around the nucleus
The nucleus is way smaller than what he proposed. And the neutrons would be a little under 2 miles away from the protons if the proton was 1 foot away. Also, protons are about 1835 times larger than the neutrons...does this help?