In 2008, according to the Bureau of Transportation Statistics, there were approximately 810,000,000 passengers in the United States.
According to a recent study published by UCLA, approximately 0.3% of the population is transgendered.
Applying the two figures (810,000,000 x 0.003) suggests that 2,430,000 passengers were transgendered.
I could not find similar statistics for numbers of passengers who flew to, from, or within Canada.