That the support for Ahmed the Clockmaker was shown as a way to show Muslims that not all Americans are stereotyping racist yokels.
That is several stereotypes: all Americans are racists, all Yokels are non-Muslim, Muslims are not American. Stereotypes themselves are not inherently racist, they're generalities based on characteristics that among others may include ethnicity and national origin. Birds can fly, Basketball players are tall, the French are mean etc. A racist makes judgments on based exclusively on ethnicity. It's evident by the previous response, and unlike the other poster, that Muslims aren't from specific racial backgrounds. Unless $religion is tied to a specific ethnic group, it cannot be argued as racist. Not to mention people wouldn't be able to convert to it. There's a very big difference between discrimination based on what people intrinsically are, and discrimination based on sets of ideas that people sign up to.
Hatred of specific religions, racism, it's all bigotry. And most people aren't bigots. Fortunately, the ones that are like to shout it from the rooftops. It makes them easy to spot.
Couldn't agree more, although I'd expand specific to all, and not all bigotry is hatred.
tl;dr some racists are also anti-Muslim, anti-Muslim != racist. Muslim is sometimes used as a shorthand for middle-eastern brown people; the ones who aren't jews (who are all white, of course). Confusion stems from implicit code for "those brown guys" vs people who believe Allah is God.