How does Apocalypse withstand a supersonic beam that defeated the Juggernaut?
Firstly he has a disintegrator beam, that we have seen him use to vapourize a steel 'I' beam. A disintegrator beam usually works by attacking the atomic bonding present in the material.
The second point for Nimrod, is that after analying his superhuman opponent, he can create weapons systems to overcome his opponent. Given time, he can come up with focused weapons to target the weaknesses of his opponent.
He is from the future and his tech is very advanced.