Wood floor protection during demolition of roof
It would be very worth investing in at least two layers of protection. I'd start with something that will accommodate dust and debris. It should seal against them, but it should also cushion them if they do work their way in. There are some felt-lined plastic products to be found, and there are some paper-based products that would do as well. Roll them out and tape the seams. Also tape the perimeter with something that won't leave stains or residue. 

Next, buy a stack of inexpensive sheet material--1/4" OSB, luan plywood, or cdx plywood. Lay it out to cover as much of the area as possible. Overlap if necessary. Place the nicer face down to preserver it for re-use or re-sale after the project is complete.

It might then make sense to tarp over it all as a  debris-collection mechanism, so that you can pick up at the end of each day and shake it out elsewhere. Debris management is as much a part of the equation as the protection itself. You don't want plaster or masonry crumbs, loose nails, etc. on the floor longer than necessary. 

Finally, give the area a good vacuum cleaning whenever you can work it in. Nothing beats suction to pull damaging debris out of tight places.