First of all, you need to know this basic thing, there are two types of Kanji reading in Japanese, the first one is called "Kunyomi", which is the original Japanese reading for the kanji. Most of the time, IF you SEE a kanji STAND ALL ALONE, and you use the "Kunyomi", IF you SEE a kanji GOES WITH ANOTHER KANJI, then you use "Onyomi", which is the "Chinese-based reading". And NOTE that this is just "MOST OF THE TIME", there are exceptions. And this 本 just happens to be one of them.
This 本, of course, its Kunyomi is "moto", and its Onyomi is "hon".
So for example, there is a book on the table, and I say: これは本です. See that? It stands alone, there is no any other Kanji next to it, so you should read it as "moto" right? But no, it's still "hon". Because in Japanese, "hon" means book, any I'm talking this book. The context is important.
So the bottom line is....you need to learn the words....for example "hon" is "book", so when you see 本, and the context is certainly about a book, then you should certainly read it as "hon". Please, Kanji just represents the word, don't be confused by their "readings". To illustrate that, I'll show you one more example, and it's even more intriguing. It's the word "田舎”, it's read as "inaka", and it means "rural area/ countryside". But the funny thing is if you look up both of these two kanji, you'll see that 田's Onyomi and Kunyomi are "den" and "ta" respectively. There is no "i" or "ina" whatsoever. The same for 舎, there is no "ka" or maybe "naka" whatsover.
That's why I said the kanji just represents the word. 田 means "ricefield" and 舎 means "cottage"
"ricefield" + "cottage" = "rural area" (makes sense), and what is "rural area" in Japanese? It's "inaka"
That's the process of how you would read. Those "Onyomi" and "Kunyomi" are just there to HELP you SOMEHOW COME UP WITH A WAY TO READ the UNFAMILIAR kanj, you don't use them to decide how to READ kanji.
I know my answer is long right, but well, can't be helped. Good luck.