If neutrons decay into proton, electron and (anti)neutrino of electron type, then is it safe to say that atoms are protons, electrons and neutrinos?
No. The decay products of a certain particle are not equivalent to its constituents. This is evident especially in the context of fundamental particles: quarks can decay into other particles, but that does not mean that a quark is not elementary (see my answer to this question).
Nuclei are made of neutrons and protons, which in turn consist of quarks and gluons, and hence, on an elementary level, atoms are made of electrons, quarks and gluons.