Yep.
Actually, things will calm down and relations will improve between the US and Germany now that Merkel is Chancellor. What most Europeans don't realize is that the Internet now connects us and we are watching. Where in the past it made good local politics to bash the US since we mostly ignored Europe, we are now paying more attention to you.
Regarding Gitmo, I believe there are two issues that are being combined resulting in some confusion.
1) Treatment of unlawful combatants
IMO, this is the easiest. Basically, an unlawful combatant is one that doesn't identify themselves (with a uniform) and doesn't limit themselves to military targets.
These people are not subject to the Geneva convention. According to the rules of war, they can be summarily executed. We have chosen not to do this (and it really is not an option politically) and instead put them in a military prison.
2) Determination of who is an unlawful combatant
This is the sticking point, IMO. We say that we are at war and as such, captured combatants will get a military tribunal, not a trial. These people do not have the status of Prisoner of War because they were unlawful.
You say that these people could be innocent and should get a full trial to determine their guilt and innocence.
This is a tricky issue. When you are at war, you can not give every captured enemy soldier a trial. By the same token, no one wants to condemn innocent people. I think some sort of middle ground is needed, maybe the evidence presented at the tribunal needs to be made public. I don't know.
However, I hope we can both agree that the terrorists have caused this problem because they are an organized, international organization yet they hide in the civilian population.