If this is a one-off project, then I too would use Family Tree Maker to make the pedigree charts. InDesign is great for most layout purposes, but not in this instance. InDesign can be used for the rest of the project (i.e. tales and anecdotes from the family etc) but the pedigree charts will be easier to do in FTM.
For my own family tree, all the data was plotted using Ancestry and then exported as a GEDCOM file and imported into free Mac software called Gramps.
My employer has an application especially made for it that takes a GEDCOM file and transforms it into text that is easier to manipulate in InDesign. This software is not off-the-shelf, it was created by a family tree enthusiast and is a bespoke application. That said, the software is running in DOS and we're looking to find an XML-based solution before the software can no longer run. However, every expert I've asked at the conferences I've attended in the last three years say the same thing when I mention this issue: "What's a GEDCOM file?". If anyone from Ancestry.com is reading this, I'd be interested in a PM.
Similarly, if I was preparing a Chemistry book, I'd rather use Chemdraw to draw the organic compounds rather than illustrator; and if I was setting up a book of sheet music, I'd rather use Sibelius.