If the bike shop is one which you visit often, and are a regular customer, then my expectation would be that small items of labour would be either tossed in, or heavily discounted. If you are not a regular, then I would expect them to charge for installation of something like a pedal, but not for a job which they could not do.
At the same time, I expect to pay more at the LBS than I would over the internet for parts, specifically because of the staff, the expertise and the local stock.