Well, in most cases when the military takes over, they state that the control will be given back to the people, once bla bla bla will happen.
However, as I understand the situation in Thailand, it seems that the Thai people is somewhat pleased about Thaksin being replaced.
Another thing to take into consideration is that Boonyaratglin didn't challenge the king, and still answers to him. The king is extremely revered in Thailand, and hopefully he'll take an active role in restoring democracy to the country, as he did in the past.
I spoke to a thai friend this morning, and he said that once the uncertainty around Thaksin return from NY will evaporate, most thais believe that the military control will continue untill the scheduled elections due next year.
As for me, I'm not changing my flight plans to thailand for the beginning of october... :)