Is Cleveland Clinic making McDonald's a scapegoat?

McDonald's is getting the boot from the Cleveland Clinic food court even as other fast food chains remain.

The hospital chose not to renew its lease so the restaurant will shutter next month. Still, other fast food chains, including Au Bon Pain and Moe's Southwest Grill, will continue to operate there.

Ron Antonelli | Bloomberg | Getty Images

The hospital says its goal is to reduce risk factors that contribute significantly to chronic diseases, and the action is not about any one restaurant but rather a move toward a healthier overall environment.

Moe's, in particular, has entree combinations that can be high in calories. A 12-inch flour tortilla clocks in at 310 calories, more than a McDonald's hamburger at 250. Meanwhile, Au Bon Pain has sandwiches that top 700 calories, more than the 540 that a Big Mac includes.

Read More Restaurants' secret weapon: The burger?!?!

Dr. Barry Popkin, the W. R. Kenan Jr. distinguished professor of nutrition at the University of North Carolina, Chapel Hill, says McDonald's has become a "symbol" and scapegoat for bad eating habits.

"It's more the consumer than what they're selling. You can find healthy options at any of them," Popkin said.

Rare case for McDonald's

In an email, Moe's Southwest Grill President Bruce Schroder wrote: "Because everything on our menu is customizable, guests can create meals based on their unique tastes and lifestyles. We help them make informed decisions by being transparent about our ingredients through our online nutrition calculator and attributes that are posted on the walls of our restaurants."

Read MoreMcDonald's just topped a key new poll

Au Bon Pain defended its presence, pointing out that it eliminated trans fats and posted calorie counts on its menus long before any laws required it.

"Au Bon Pain has always been committed to a balanced menu, with choices for everyone from the most health-conscious to someone in search of a little indulgence," said Maria Feicht, the chain's chief brand officer. "We have long been recognized as a pioneer in the healthful fast casual dining industry."

A spokesperson for the hospital insists McDonald's is not being singled out.

"All I can tell you is that there are many more changes to come. Can't provide specifics at this time. McDonald's is not singled out. They had a 20-year lease with us that expired," wrote Eileen Sheil, the clinic's executive director of corporate communications, in an email.

The location's owner/operator Turan Strange issued the following statement: "My family and employees have enjoyed serving the Cleveland Clinic community for the past 20 years. All of the employees at the clinic restaurant are being offered opportunities to continue working in other locations within my organization. We invite families and residents in the hospital community to visit our other Cleveland-area restaurants for the variety of balanced choices of food and beverages that we're proud to serve."