We usually do not charge shipping, not for tubes and tires that we should have in stock anyway. Some things however, need it next day, we charge. Order a Yakima Rocket box, we charge(Comes motor freight shipping is over a $100) Order something really heavy, say a two arm Park stand which is over a hundred pounds, we charge.
Your shop was unfair, the real deal with paying more in a bike shop, other than the knowlegable and friendly staff, is that the stuff is right there for you to take home.
On the other hand just about all mail order places charge shipping and I have a ups rate book so I can say with some authority they are making nice margin on shipping.