It looked a nit uncomfortable for the Chancellor, but as you said, no malice seemed to be behind it. Just not the most appropriate thing to do, I guess.
My take on Merkel's expression was entirely different, and here's why.
In my family, we do a lot of shoulder rubbing, call it a family tradition, (it's probably because we all carry our "stress" in our shoulder muscles.)
Anyhoo, if I were to rub my sister's shoulders, like Bush did to Merkel, she would make exactly the same gesture...why...because it hurts her, and she reacts just like Merkel, raises her shoulders, throws her hands up and then pushes the "shoulder rubber" away.
When I saw the photos, that's immediately what I thought of, the poor woman must have had a bad shoulder ache (perhaps mentioned it to the Prez) and when he grabbed her shoulders and started rubbing, it hurt like heck, so she reacted to the pain.
May not have been the case at all, but that's what I thought of when I saw it.
LOL, I´m wondering what all this fuss is about! Really.
German newspapers comment not on the President´s gesture but on the reaction of the American news and web-users. It was meant as a friendly gesture by Pres. Bush, but it´s clearly visible that Merkel was surprised and didn´t like it until she found out it was meant funny. No problem at all, let´s go on.