Noseall, you seemed to have changed tack on this in a short time!
You are quite right - there are times when "taking a risk" is the prefferred option. But as for not loading the quote with "just in case pricing" you dont have to. You explain the issues, and the cost, if any, of protection. The client then makes a choice, and I have lost count of the times where the punter has responded with "don't worry too much, we will be changing the xxxx in a few xxxx time, we can live with it", or similar. But you MUST record this in some way, I make a note in the quotation preperation, to avoid any later dispute. I had a client once making a big deal about me asking him to move his car of the drive, for me to access with fireplace etc. I asked what the problem was, and he said he did not like leaving his car on the road. This was a quiet side street with no parking problems!. I pointed out that there is a chance that I would dent or scratch his motor, and that I would need to make a little note for home to sign. So he moved the car, and was as good as gold thereafter.
Until recently, my daily work involved chopping out fireplaces, draining down radiators and digging floors - all of which carry a risk of "collateral damage". At the quote stage, I would assess the site, and explain possible repurcussions with client, and the methods required to avoid damage. I have never suggested lifting a parquet flooring temporarily!, but in the work area, dust sheets would go down, with thin ply on top. If potential for "wet", then plastic sheeting goes down before the dust sheets. It is a total pain, but a million times better than being in the OP's builders position. The most frustrating thing is that after taking the precautions, everything goes smoothly and the precautions seemed unneccessary. Occasionally there are high traffic areas, with, restricted access. It is sensible to point this out and explain that although care is taken the house WILL be a "work area", and some damage may ensue, such as snagging plaster on a tight corner when moving kit in and out. The same goes for when a punter has the house decorated, then decides to have a fireplace fitted (which happens more than you would think). Again the "work area" is mentioned and we cannot guarantee there will be no marks on the new paint.
Occasionally one does get a customer where all this is too much, and flagging the problems can lose a job - but, frankly, these are the sort of punters best avoided 'cos there WILL be an issue, and they will refuse to see your POV.
I also agree with the comment about site workers, and I have seen this many times. "Site" guys are generally different to those who have been trained in occupied houses. They often cannot "see" the potential for problems, as on a site there are few, and there is generally someone around to fix any damage, say a plumber gouging a chunk of plaster out of the wall when carting their kit through.
To sum up, the OP's problem with the floor was entirely predictable, and avoiable, and anyone suggesting that it is an acceptable and inevitable hazard of having work done so is being a little disingenious.