Nietzsche often uses the same word to mean different things. When he uses the word "nihilist", he could be referencing three separate ideas:
1) Christian Nihilism - the negation of life and movement toward nothingness; Christianity does not feel itself to be nihilistic, but from the atheistic perspective Nietzsche has, it aims toward nothing and denies life. While the atheist has only life to value, the Christian decides that this life we live now has no value, and only the life beyond has meaning. However, since that life is non-existent, Christians value nothing at all.
2) Negative Nihilism - the realization that the universe is a cold and unloving place, and thus the belief that one's life has no meaning. This is the kind of nihilism the OP is talking about, and it is a nihilism that Nietzsche is fighting against because he believes that it is a natural post-Christian tendency.
3) Positive Nihilism - the realization that the universe is a cold and unloving place, and that is perfectly fine. While life has no objective meaning, the positive nihilist has come to realize that the valuation of the universe takes place solely within his/her own mind, and he/she can choose what meaning life has. This is could also be called a "happy nihilism", because the burden of God has been destroyed, but the shadow of God, negative nihilism, has been destroyed as well. What is left is a love of life.
I think the main reason people struggle to read Nietzsche is that they do not catch these subtleties; Nietzsche does us no favors, and uses the terms interchangeably. His goal is not necessarily to help us understand him, but rather to create introspection.