Brennan wrote her first book in order to cope with her relationship (or non-relationship) with Booth. (At least, that was part of it.)
This probably sounds like some crazy shipper delusion, but hear me out: in the Pilot, Brennan comes back from Guatemala and she already has a book published, which had not been published in the 100th episode flashback. Therefore, she must have written the book after the case with Booth and before she went to Guatemala, giving her only a few months to write since she was in Guatemala for some time (two months, was it?) and only 11 months total passed between the two cases that she worked with Booth.
Thus, either she writes like a speed-demon, or she began her book immediately following the case she worked with Booth.
AND at this point in the series (I just finished episode 5, the Boy in the Bush), we're starting to see what a big part of the book Agent Andy, who is based on Booth, is... meaning that even though they fought, Booth (and the whole experience of working on that one case with him) really stuck with Brennan, prompting her to write that book. Or prompting the content in the book. (We don't know why she began writing the books. Any thoughts?)
But either way, Booth was on her mind-- he was, in a sense, her muse.
So, why, in the Pilot, was Brennan reluctant to work with Booth again? I can think of many reasons, but here are a few:
a) She insists that her colleagues are NOT depicted in her book; she's in denial, or simply not consciously aware of the fact that they ARE.
b) She's a tough gal and never wants to give in easily.
c) She IS aware of her feelings and what she's done (I have no evidence of this, however); she's coped and now she wants to move on.
d) Some combination of two or three of the above reasons.
Thoughts?