Beside the obvious, they typically have a smaller foot print, they donate more to the community, and they care more about their community. I know this from experience.
One big thing I noticed for let's say restaurants is, they try to feed you non-processed foods while corporate will make their own heavy process foods because they can save money across all their restaurants.
Boutique hotels have a better history and a better story.
Small businesses create the culture for the communities they are in, so respect them as much as a they respect you.