Learn Russian: Почему вы отменяете этот рейс?

This is a great prompt to practice из-за (because of or due to). We use it for negative or external causes. Since canceling a flight is an unfortunate event, you could answer: Из-за плохой погоды (Due to bad weather) or Из-за снега (Because of the snow). Just remember that из-за must always be followed by the Genitive case.

Why is the imperfective verb отменяете used here instead of a perfective form?

отменяете is the present tense of отменять, meaning the cancellation is happening right now. Perfective verbs in Russian do not have a present tense. If you used the perfective form отмените, it would shift the meaning to the future tense: Why will you cancel this flight?

Why does этот рейс look exactly like the dictionary form? Shouldn't a direct object change for the Accusative case?

It actually is in the Accusative case! For masculine inanimate nouns (non-living things like a flight), the Accusative form is identical to the Nominative (dictionary) form. Because of this rule, both the noun рейс and the pronoun этот keep their basic endings here.

What is the difference between рейс and полёт? Don't they both translate to flight?

Yes, but they are used in different contexts. рейс refers to a scheduled commercial trip, route, or service, like an airline flight or a scheduled bus route. полёт refers to the physical action or process of flying through the air, like a bird flying or the sensation of being in the sky.