The 12.99 really isn't that bad. Look at the actual cost per mile to operate a motor vehicle. Plus the tax you would pay at a local store if they even have what you need.
I feel your pain with the shipping but it really isn't bad when you consider "It comes to you". I will almost always pay the extra on shipping since it saves my time from driving around town and remember, The extra miles put on your work truck cannot be taken back off. One thing I always do is, When I go to write an estimate, Once I figure what I have to make on the job, I almost always add a $25.00 charge on top of everything else. It helps to cover the little extras.
If you don't feel you can get away with adding an additional $25.00 into the price of the job, Try slipping in a $5.00 or 8.00 "shop supplies" charge into the next jobs which will cover the shipping for a small order. Every Auto shop does it and almost no-one questions it!
Mike