"Airplanes also fly in the sky."
The particle を can also be used with action verbs and translates to something like 'through', for example: 森を歩く (mori wo aruku) means "to walk through the forest." The forest is being walked through, so the verb still takes the forest as the direct object. I hope this helps/makes sense.
The subtle difference between using the ～て-form of the verb (とんでいます) vs. the standard polite form (とびます) is that the て-form indicates an action currently in progress. E.g. 「ひこうきがそらにとんでいます」 means "an airplane is flying through the sky" (like, right now) while 「ひこうきがそらをとびます」means "an airplane flies through the sky" which is more indicative of a general behavior rather than something happening at the moment.