There was a point in its history when Islamic countries were the only countires that preserved and advanced Greek science, philosophy and mathematics. Modern-day mathematics owes a great deal to early Islamic philosophers, and as nungate mentioned, Islamic rule was comparatively civilized compared to medieval Europe.
I'm at a loss, however, to explain what has happened to the Islamic world since - today virtually no scientific research whatsoever takes place in the Islamic world, and it seems to be synonymous with virulent homophobia and female subjugation - even in those majority-Muslim countires which are nominally secular.
And no, I don't see that the charitable activities of any faith (including the catholic church) necessarily balance them out. These are acts of conditional love - quite a vile and insipid idea if you think about it - and in the case of the Catholic church has come with great big heavy destructive strings attached.