Thailand is worth the flight time
Thailand is an amazing place with incredible history and geography. For the most part, people are very warm and the society is socially conservative especially the further you travel in-country. Bangkok sort of sucks, but its central location makes it a fantastic jumping off point for any locations in Asia.
The ladyboys are no big deal and you'd have to be super messed up not to know they aren't women. Thai society loves them and treats them with the same respect as other citizens. Many are not sex workers and have regular jobs. It takes a few months to get accustomed to seeing them, but the shock wears off quickly. My biggest issue with living there was the heat...it's unrelenting especially in Bangkok and the countryside. However, Bangkok's entertainment venues, shopping and restaurants are exceptional.
Southern Thailand is beautiful and worthy of your time. Muslims live all over South East Asia and I have never had any issues with them
They are hard working family oriented folks. In a nutshell, you have to keep out of bad area's, respect the culture, and stay far away from drugs and idiots. Some area's of South East Asia including parts of Thailand should be no fly zones for travelers. Better safe than sorry, but we're talking about huge countries with so much to offer, why put yourself in jeopardy with too much to see in a lifetime?
Oh and the women...the women are beautiful. Enjoy!