How to throw a bike on to your shoulder smoothly and start running is not totally intuitive. For the best explanation I've ever seen, watch this video of Brandon Dwight (Boulder Cycle Sport shop owner and veteran racer). My bike has a non round top tube which cuts into the shoulder rather fiercely and feels like this when you pick the bike up and plop it on your shoulder at a stand-still:
Fortunately, while running, it isn't nearly so bad and your fore-arm takes a lot of the load. Even so, one racer I saw needed a little extra help and turned to some foam pipe insullation for a little extra cushion. Perhaps she'd recently suffered a broken collar bone?
Photo from http://www.antique-used-tools.com/