In my stories, when characters are doing something casually, I'll use a real business just to save time. Everybody knows McDonalds, everybody knows what McDonalds serves, and if I have a character go there, it's to show they got food and continued on with their day.
If it's something special, a place where a character is employed, reservations at a restaurant, whatever, I think it's far more fun to exercise the imagination a bit. Why have my main character in "Crash Into Me" go to Starbucks when she can instead visit "To Bean or Not To Bean", an indie coffee house, where the girl behind the counter knows her order and buries her nose in a true crime paperback when there aren't any customers? It's fun, it's world-building, and it engages the reader without them even realizing it.
I've never written anything libelous or defamatory (or even scandalous) about a business in my works though, so the old 'YMMV' applies.