I don't think it's a McDonald's endorsed project. Google McRide, and you get this thread and another similar one on another forum. McDonald's would either keep the project completely under wraps or have something about it online. But that doesn't make it sinister.
I love that the questions are all about "your local McDonalds" I only visit McDonald's on my bike when it is cold, dark and I am in search of something warm and dry. Oh, and a clean toilet. If I was at my local McDonalds, I go home for all that.
I love that if you go into a McDonald's in the middle of a carpark/retail park at 4am on a Sunday morning, no one cares that you bring your bike in. That's never going to be company policy, and if attention is drawn to it, it might become explicit company policy not to allow you to do so.
If they want to talk to people who cycle to their local McDonalds they need to talk to teenagers hanging around there after school ("Chunder chicks", as we used to call the girls that did that.)