Because Flake does't disagree with the republican party on many substantive policy issues, and Trump's policies are mostly in line with standard GOP stances. Flake's speech was a callout to the party regarding its attitude of hostility and anger toward the left, and toward minority groups they are scapegoating for the nation's problems, of which he sees the rise of Trump as a symptom.
Flake is solidly conservative, no doubt. I think his voting record is even more conservative than the average GOP senator. But Flake thinks Trump is unfit to govern, that he's embarrassing the country with his erratic foreign policy, constant childish behavior, and his dishonesty. As I already said, I think Flake should run rather than pullout, and he should run on a platform which is critical of Trump, even though he thinks he can't win if he does. So I don't think Flake is exactly a paragon of political courage.
However, consider what over 90% of the GOP in Congress is doing in relation to Trump. Nothing, that's what. Many of these people know that Trump is a terrible president and they're saying nothing at all. I think there's value in conservative republicans going on record criticizing Trump. Because of that, I don't think it's terribly pragmatic to treat someone like Flake with hostility as some libs are doing in this thread. When someone is speaking the truth, which Flake has done in this speech, this should be acknowledged and encouraged.