It seems correct to me as a conditional statement about a possible future event.
Were it a certainty that the flight would take place in the future, you could say:
I will make sure you have a good flight.
In your example though, there are two different things that are uncertain. Firstly, it seems the boy isn't sure sure that he will fly. Secondly, the girl is unsure that she will get the opportunity to help the boy enjoy the flight. Both are conditional on each other, because the boy wont fly without the girl's help, but the girl can't help him unless he flies.
If the boy was flying anyway, then you could say he is going to have a flight. However, he isn't certain, so the girl is speaking in terms of if he had a flight.
In fact, you could write the sentence in the third person as:
If he had a flight, she would make it a good one.