The rules don't provide any way for the average character to do this.
While it's theoretically possible to jump up to the altitude of a flying monster, one would need to be able to stop in mid-air for long enough to make their attack, and without some outside help (e.g. some form of flight, tree branches to cling to, etc), characters just can't really do that. A jumping Charge also wouldn't work, since the character would still be unable to end its movement close enough to the enemy to attack it.
If the monsters lacked any ranged attacks themselves, the melee PCs might consider readying actions to attack the flying enemies when they come in range to attack. Otherwise, the situation ends up being a hard lesson in melee characters always bringing a ranged option (hopefully the DM goes easy on them the first time).
Of course, as usual, the DM can always adjudicate their own solution with a house rule, like you did. Seems reasonable enough. Though I'm not sure what good the attempt would do in the first place, considering you'd need a DC 50 Athletics check just to get 5 feet off the ground with a high jump, or 25 if you can somehow get a running start with your charge.
Regarding the question of a jumping Charge:
The rules provide no more support for a charge using a high jump to reach a flying enemy than any other form of jump attack. Despite being a single Standard action involving both moving and attacking, the two portions are separate and distinct. The move must be completed before the attack can be made, just like any other power that allows you to move and then attack without explicitly stating you can attack in the middle of the move, and so you must be able to stop your movement in the final square of the charge.
Ending the move in mid-air leaves you in an invalid space, whose consequence is falling, which thus happens before the attack portion and occurs effectively instantaneously (assuming high-altitude fall rules aren't relevant to the situation). If it were possible to charge into mid-air and make an attack before falling, it would also be possible to make a charge ending in an ally's space and attack before the consequences of ending in an invalid space occurred (in this case, forcing you back to the last valid space you occupied). It should be clear that this is not intended as a possible use of a charge attack.
Another less-obvious side effect of assuming the rules allow a jumping charge is that falling does not provoke opportunity attacks, unlike normal movement, and thus the charging creature would be able to retreat from the enemy without consequences after completing its attack.