Al-Awlaki is cited because he was the first US citizen to be targeted under the policy. The criticism isn't about whether he was guilty or innocent, it's about the flagrant disregard for due process.
It's important to talk about cases like that precisely in order to confront the brainworms of, "He was probably a terrorist so who cares?" That mentality is precisely what got us here and it's impossible to fix the problem without firmly rejecting that way of thinking.
You don't get to give the government permission to ignore due process in some cases and not in others. That's not how laws or systems work. Either they have to follow the process even when you personally think the person is guilty, or they can ignore the process even when you think the person is innocent. Once you've given the executive the power to make the decision unilaterally, you don't get to challenge that decision. Because that what having the power to make a decision unilaterally means.