Removing the flags was a stupid thing to do, but I suppose if I could see the situation from his eyes I might feel differently, hard to say.
I've always had a somewhat negative association with that flag, as it does to some degree represent slavery. However, I try not to pre-judge others who display it since I don't know the whole story, but I tend to assume (wrongly I'm sure) that most I see on cars, etc. are there just to get attention and get a rise out of others.

In the case of a confederate soldier I can understand it being displayed on the grave, at least to a degree, but certainly if it was put there by the family or the person requested that it be on their grave, for whatever reason, than the opinions of others is a non-issue.

I feel the same way. If someone feels I need to have a grave, it should be small and either contain my cremated remains or nothing at all (just symbolic). With all due respect, the idea of having something like a mausoleum or a huge plaque at your grave site (usually chosen and paid for by the person themselves) seems high on the list of douchey things a person could do.