There are online stores that can sell you Specialized, Giant and Cannondale bikes. Trek supports their LBS franchises so that is harder. But there is a great advantage in visiting a LBS and that is service. At a big box store the person that puts your bike together quite often has no more or maybe less bicycling mechanical experience than the customer. So it is a coin toss that you will get a bike with proper spoke tension or even proper shifter adjustment. An LBS will more than likely check out all of the bike assembly and can often change some things if you wish before you take the bike home. If you happen to have a defective bottom bracket from someplace like Bikes direct your options are limited. Often people end up taking a big box bike or an online bike to an LBS to get things adjusted anyway. One of my LBS makes more from working on just those kinds of bikes than they do servicing what they sell.
But the biggest difference may be the quality of the components. Wheels are often where mass market bikes skimp and wheels will make a big difference in ride quality of most any bike.
Once people know what they want or have experience with cycling online purchases can save you a lot of money. But still having a good relationship with a LBS can be worth more than someone realizes till they have something break that they do not have to tools to fix.
And Schwinn has been improving over the last few years and even are now offering some LBS quality bikes.