Hatred might be too strong a word, especially if the criticism of religion (and I mean here organized religion, not any simple belief), opposing it and decrying its evils, can be demagogically conflated with hatred towards believers, a fallacious identification many use in order to create an emotional confrontation beyond facts, arguments and evidence.
So rather than "hating" I would say "strongly oppose". And some (or many) atheists oppose, criticize and expose religion for the same reason that many theists do. Belief or unbelief in a deity is not a prerequisite for being aware of the many wrongs and evils of religion, the hatred it induces in people and its sad results.
Atheism is a philosophical and rational stance: atheists cannot believe in any deity because of the lack of evidence on its existence. Anti-religionism or the criticism of religion is also a moral stance based on the harm that belief has on people's lives, on societies and on human dignity, on the worst teachings of religion and on the suffering both of the faithful (as in the case of children raped by priests) and of the faithful's victims (as in the massacres of Rwanda and the genocide by ISIS/Daesh).
A "belief in what isn't science" is not a good definition of religion. My love of Bach and Hieronymus Bosch is certainly not science (at least as of now), but it is not religion. Mysteries to be solved by science are not religion, either. Religion implies the belief beyond reason of a set of preternatural statements, obtained through divine revelation and which are not subject to criticism and which are imposed upon the faithful and/or the unfaithful.
It isn't hatred of religion. It is opposition to organized and formal religion. However, when atheists say that they themselves don't have religion in their atheism, they are either ignorant of the dictionary definition of "religion," or they are liars.
