There are certainly aspects of this story which constitute a criticism of patriotism, but the story as a whole has a very different message.
Of course, during the devil's arguments, the story seems to be a criticism of patriotism. The devil very accurately points out that very many evil things have been done by Americans and that there have been many evil Americans. This would seem to be a critique of patriotism because it points out that America is no better of a country than any other.
However, the way that the story ends is certainly not a critique of patriotism. Webster shows true patriotism -- he recognizes his country's faults but he argues that they are outweighed by its virtues. The fact that his argument wins the trial clearly shows that Benet is not trying to argue against patriotic sentiments.