It is fine but I am sort of curious now that you had posted this question. Hopefully someone will fly with one of these soon!!
Just landed in Vegas after flying in from Chicago. I put it through the scanner without removing it. I had both my MBA and my iPad with me. They stopped the belt, took out my bag and told me to remove it from my bag next time. They left the iPad in the bag for the re-scan, however.
I don't have one of those TSA-checkpoint-friendly bags at the moment. That would have negated this interruption I'm sure.
I've got the 13" MBA...I'm pretty sure the smaller 11" netbook model would have been treated the same, however.