As long as you resemble and present yourself as the person depicted on your ID, you should be fine for domestic travel. Though I only fly 4 or 5 time a year now, I've never had a problem.
Regarding international travel, additional documentation or an explanatory letter may be be helpful if you run into a sticky situation, however if you're only a few months into HRT I really don't think you'll have any issues. When the TSA/customs people look at your ID and then at you, just give em' a goofy smile and they'll usually just snicker and send you on your way.
Travel "security" has come a long way since the years immediately following 9/11. Those were some truly horrible times, especially since I often had to fly 4-5 times a week, sometimes multiple flights a day.