Is there any reason other than vengeance for Ishbalan, whose people were exterminated by Military, that Scar set out to exterminate State Alchemists instead of exterminating all Alchemists?
This is all based on Scar's train of thought, and own decisions. However, I respect his decision:
The fighting continued to spread until the entire East Area of Amestris had become a war zone. In 1908, a full seven years after the conflict had begun, Amestrian Führer King Bradley issued Order 3066, sending State Alchemists in to the front lines to act as human weapons. Ishval Civil War - Fullmetal Alchemist Wiki
So, as we are told in Fullmetal Alchemist Brotherhood (throughout the series, no specific episode(s)) - it was the State Alchemists that were taking part in the war, therefore it was the State Alchemists which the Ishvalans should hold their grudge against - the State Alchemists who murdered them, fought with them, and harmed them.
As I said, however, it is based on Scar's decision. It makes sense as you'd want to avenge your friends by harming the person who harmed them. In this case, he went a step further as to attack those who hold the title of State Alchemist, even if they didn't participate in the war. Why he went a step further in that direction and not attack all Alchemists, is just be how his rage works.