I think its important to also consider the line directly precede that one that goes "Whoever fights monsters should see to it that in the process he does not become a monster."
I have read a ton of Nietzsche, but almost no commentary by other philosophers on him (except for Walter Kaufmann's notes on his translations) so I could be way off base. Many of Nietzsche's maxims are part of larger themes in his work, but I'm not so sure this is one of them--although it does fit in the grand scheme. Lots of them are simple observations (phrased in beautiful language and metaphors, of course

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I think that here Nietzsche is simply cautioning his readers not to get wholly wrapped up into whatever they are tackling intellecutally. In
The Gay Science he tells why he hates of enduring habits, and in
Thus Spoke Zarathustra he tells us to reject even his own teachings. Here I think Nietzsche is saying that, especially in criticizing something, don't become like that thing yourself.
Many atheists here criticize christianity constantly, but by doing this its very possible they pick up the very habits they are disparaging. It happens all the time in reality, if you think about it. And considering Nietzsche almost always used the dialectic, I think this makes a lot of sense. When two ideas clash, the losing idea always influences the winning one to some extent. Just don't let it influence you to the point where the very thing you hate is what you become without realizing it.
One last note is that Nietzsche urges not to be nihilists, not to question everything all at once... but to simply give nothing
permanent immunity against questioning. Be in a static state and watch out for this pitfall.