Quite a few reasons exist to choose hotels over bed and breakfast. One of the most critical factors is simple economics: supply and demand. There are a far fewer bed and breakfast. Furthermore, bed and breakfasts hold fewer guests than hotels. The bad news is that bed and breakfasts usually charge over a hundred dollars a night. With Hotwire and Travelocity I have stayed at 3-star hotels for sixty dollars or less. In other words, hotels usually provide guests with more bang for the buck.
Bed and breakfasts have other downsides. There is little privacy in a bed and breakfast. Many people vacation to get away from other people. Also, there are more efficient ways to complain to national chain hotels. If you get bad service at a bed and breakfast, then you are out of look. With a national chain, you can usually speak to a manager or someone at a national office.
What about standards and reliable service? Some hotel chains provide great service to uphold their reputations. Picking a bed and breakfast can involve a lot of luck. On the other hand, I know that a Renaissance or a Radisson will usually provide me with great service.