Spoilers, eps 1-30. Everything in this that you haven't seen in episodes 1-30 is 100% conjecture on my part. Don't quote me. Or, do. I'm not going to tell you what to do!
Or, rather, Val suspects:
15 years ago, Cheryl (that would be Bruce's wife, Bruce would be Scar's brother, and yes, I made those names up) died. Bruce tries HT. He loses NOTHING as far as we know. We all know that someone is watching the entire country for signs of HT.
Very shortly thereafter, the war is started. By machinations, I believe. That is, I believe that the military shot a kid on purpose (making it look accidental) so that Ishval would revolt and then they could say "Oi, they started it!" while they clean 'em out.
Dr. Marco told the tale that it was a massacre. Not a war at all. And why use the incomplete philstones to launch massive attacks at the enemy who is barely armed with rifles?
Because the Ishval people hold the key to going through the Gate without paying the toll!!
Here's further evidence. Color has been rather symbolic in the show. The red water, blood, Ed's red coat... surely it's not a coincidence that Ishval are characterized by red eyes.
Bruce, when he first tries HT, he is upset about the results but he doesn't seem like he's lost anything. The only thing we don't see of Bruce in the tattooed scene is, well, I'd like to not think he lost THAT. o_O Sure, he's insane, but he had to be insane in the first place to not only use alchemy which is against his religion but to use it for human transmutation, which is against EVERYBODY'S belief system. So, based on the evidence at hand, he didn't lose anything.
So, the military now knows about this, because someone there is keeping close tabs on anyone who HTs. (That's my theory, again, but it's pretty solid.) They find out a guy HTd without paying. That means that Ishval can have the ultimate power of alchemy. Which means the ultimate power in the world. Which is not something the military is keen on. But if every single person in Ishval can gain ultimate alchemy power, then they're going to have to be eliminated.
Remember when Scar was first saved by jii-san and Rick, he was very surprised there were so many survivors of the massacre. And what happens? The military (under Sloth's direction!) comes in and tries to wipe 'em out again! And now, Mr. Weaselly-mine-guy, he tells Sloth that there are Ishval people there, and now they send Roy out under the guise of capturing Scar!
Seems a lot of trouble to waste on a few refugees, don't it.
Hope I made sense. Don't hit me too hard ^_^;;