The advantage of illusory pit is to make creature prone.
The advantage of flying is to not fall prone in pit. And to stay away from land-based ennemies.
If it's unijust to deny the PC the use of their spell, it will be unjust to deny the (flying) PC the utility of his power. Things go both ways.
The flying creature is not immune to the prone condition nor is flying a simple "get away from land based enemies 100%" skill/ability. flying has weaknesses, being knocked prone while doing it is one of them. Nowhere in the rules does it say "One advantage of flying is you cannot fall prone into pits" that my friend, you made up completely. Which is fine, as long as you don't try to say that's the rules, because it's not. When you start tacking on additional rules or interpreting the written rules differently than written to suit your view of how things should work within the game you are creating house-rules. At that point you can do anything you want, but what you do is no longer germane to the discussion of how the rules actually work as written. Houseruling can be fair to everyone but that really depends on how you do it, are you changing the rule right when someone tries something and just saying, "no that doesn't make sense to me, you can't do it" even though the standard rules allow it, that's not a fair houseruling. You can do it, but it's not fair, to be fair the houserule needs to be known before character choices are made, before the conditions for the houserule come up. The real way to handle that situation is to say "wow, I don't think that should work, I'll allow it this time but after this session it won't work anymore, I'll let you change your power if you want because of this change but I just can't see that working properly in my games" That is the fair version.
Something more : the game is about finding strategies, solutions, tricks. Now, we have two choices. Either the players and the DM are trying to think "in character" or they are playing an abstract strategy game.
Someone had a very good example of how powers work. If you think of powers as in character named actions it makes NO sense at all. I'm a rogue, and I'm going to blinding barrage... Oh man now that I've done it, I don't think I can muster up the ability to do that again... for at least a day, or until I rest ofr 6 hours... What? That makes no sense at all "in character". You have to look at it as the ability to affect plot in a given way once a day, disconnect the action from the ability or in character it's impossible for martial power sources to explain dailies and encounter powers.
To each his own, that's two different style of play. They are both perfectly valid, as long as everyone enjoy them.
Myself, I can't enjoy a game where flying creature fall prone in illusory pits or where people trip gelatinous cube, where "come get some" makes fleeing enemies go backward to be slaughtered, or where a rogue can fire 9 bolts in a round with a crossbow, at 9 different enemies.
Of course, we could take 15 minutes each time one of this situation occurs to find a plausible explanation. I'd rather say say "no, try something else, it's not appropriate" or rewrite the power pre-emptively. There are far enough perfectly working powers that don't cause me headaches so that I can house-rule or restrict what I want to house-rule or restrict. And, no, it's NOT unfair to the players, because the rules are the same for all, and because this is not an adversary game but a story based game, where both players and DM collaborate to have fun and tell cool stories. And while tripping ooze maybe fun in some kind of stories, it's not in many other.
I'm not sure I consider a system of gaming where the DM adjusts things on a whim when someone tries something as fair or even fun, valid yes, fair not so much, fun maybe for the DM but not the player he just hosed on the spot. Firing 9 crossbow bolts in a round as part of a daily or encounter aoe power, totally within the rules, if you disallow it then you basically just said "sorry rogues and melee types, no aoe's for you, I know it's in the rules that it's allowed but I just find it silly" I sure hope you told that to them that before they picked any powers and tried to use them. Your inability to enjoy a game where that's allowed tells me you may be happier playing a different game or version of the game, 4e is designed to allow that type of stuff to occur, the say Yes mentality is part of the design philosopy. If you only allow rules and powers as a DM that don't cause you headaches and tell people no when they try something you don't like how collaborative are you actually being? And I would argue that your last statement of tripping an ooze fun in some and not in many others is backwards, fun in most, not in some others. And remember you didn't "trip it" you applied the prone condition, this is 4e not 3.5 The word trip is used very rarely
Silverstep level 13 fighter encounter uses it in the fluff and it doesn't knock prone, it pushes 1 square
Unbalancing attack level 13 rogue says it's sets the foe up for a tripping attack, this one does knock prone if the attack it sets up is triggered.
And that is EVERY mention of the word trip in the players handbook.
In the end play how you want, don't be suprised if a player in your game gets angry at you when you change something he is supposed to be able to do according to the written rules on the spot when he tries it, just because you don't think it should work because the fluff or name of the power doesn't make sense to you in the situation. When making his character and decisions he has the rules and his sensibilities to go by, he doesn't have your brain and decision making process at his disposal.