No, it is more like any European naming "Cesar airline".China named one of its airline Ghengis Khan?
Bit like Eastern European calling Hitler airline?
Ghengis Khan to east Asians is like Alexander the Great (a Macedonian) and/or Julius Cesar (a Roman) to Europeans. Both of the two European conquerors are well respected by Europeans regardless regions. For example, Julius Cesar conquered German land by killing lots of locals did not prevent later Germanic monarchs to take the title Kaiser (German spelling of Cesar) from Cesar's personal name, neither did the Germanic rulers shy away from claiming to be the legitimate heir to the Roman empire, (the Holly Roman Empire of the Germans). Alexander the Great conquered all independent Greek city states and Kingdom of Spartan, while all Greeks today highly respect Alexander.
Ghengis Khan is ONLY (more) negatively regarded by people to the west of China and Mongolia for religious and racial reasons, especially Muslims for the apparent reasons (Mongol sack of Baghdad which is a disaster of civilization).
The airline in question is funded by the government of Inner Mongolia. So using Ghengis Khan makes good commercial sense in serving routes from and to Inner Mongolia and between China and Mongolian Republic. It won't serve any route to Central and Western Asia.
Another thing that complicated the naming is that the Chinese name of the airline is NOT Ghengis Khan but "Tian Jiao" which literally means "The one/best son of the heaven". It was just a general term to refer to someone of greatness until Mao Zedong in one of his poem to express his personal ambition of exceeding any proceeding rulers of China where he addressed Ghengis Khan as "Tian Jiao" while stating that Ghengis Khan is ONLY able to conquer by brutal force without knowledge of presiding peace. It was since then, "Tian Jiao" is almost exclusively linked to Ghengis Khan. Therefor the choice of Chinese English translation of Tian Jiao to Ghengis Khan.