Maria Ross was quite a leap of faith for Roy. He knew very little about her, except that she was Armstrong's subordinate and she had some contact with the Elric brothers (although we don't know for sure how much he knew about that). Either way, that combined with the fact that the whole "main suspect" thing seemed fishy, was enough to give her the benefit of the doubt -- it was enough for Roy to try to save her.

Roy then conceived a plan in order to misdirect people in believing he killed Ross. After all, she was a prison escapee and the military was allowed to shoot if she were to resist her detention. Not only that, but Arakawa-sensei too told the story in such a way the readers were set to believe Roy had in fact burnt Maria Ross to ashes. However, if you've cared enough along the chapters to actually stop and take time to analyze Roy, you would've known that conduct was totally un-Roy like.

Anyway, soon Ross found herself out of inmediate peril and being escorted to Xerxes, a stop in her way to Xing.

     

Ross: Major Armstrong, Second Lieutenant Breda. Can you convey this to Colonel Mustang himself? If not for that plan, I would have been waiting to be killed. I am grateful for being able to escape with my life. If there is an emergency, please do not hesitate to call me back. To repay my debt of gratitude, when that time comes, the life that I'm hanging on to, can be made use to do something!

Amestris' military may be rotten at the core, but there's still people who are noble at heart and are willing to fight for something better, for everyone. Ross is one of those people. Roy was right in giving her a way out, and given the type of person Ross is, it's no wonder she's put her life in Roy's hands now. Ross' hope for the future, not just her own but everyone's, has been placed on her saviour and there's no doubt she'll do anything he needs her to.