Answer :

It was dishonorable for a woman to fight and I guess she committed treason. it was also a war so... casualty of war?
Joan of Arc was burned at the stake because those who captured her thought she was a witch. With such widespread fear of witchcraft at the time, the public was very willing to for her death.
However, here's another interesting tidbit of information, Joan of Arc did not actually die from being burned. She actually died due to smoke inhalation and was burned an additional two times (following her death) to dispose of the body.