The guide should be able to charge for whatever materials or services they want to charge for and should be able to charge whatever price they want. But, they should be upfront about it and not slide an extra bill in at the end of the trip.

That seems to be the issue with the OP, I'm guessing that if the guide had stated up front that there was a charge for flies and tippet then the OP would have been prepared for it or could have chosen not to make the trip.