Sorry, but that's just dumb.
Would you say the same thing about a level 1 encounter? Let's say you put some goblins with bows behind some barricades that give them cover, and there are caltrops spread on the ground in front of them.
Normally you'd have to advance across the caltrops, deciding whether to do so slowly and carefully, or go quickly and trust your Dex save, then either hop over the barricades, or try to fight them from the other side.
With flight you just fly over the caltrops, fly over the barricades, and kill the goblins. Trivial.
So....is that encounter "doing it wrong"?
This encounter is not being trivialised at all!
In the encounter you posited above, the flying PC has managed to avoid either walking at half speed to close with the Goblins, or avoid a DC 15 Dexterity save to walk at full speed through them (without stopping and taking 1 point of damage). Whoop-de-do. The exact same 'challenge' could be circumvented by a simple
Misty step spell, jumping, or a PC with a broom.
What's with us and brooms in this thread by the way?
My point regarding flight and it trivialising encounters, is that if flight is trivialising your encounters,
you're designing your encounters wrong.
You shouldnt be afraid of PCs with flight trivialising encounters, any more that you would be afraid of PCs with fireball trivialising encounters. I mean (as long as you're designing your encounters correctly), sometimes flight (or any other special ability or spell of the PCs) will dominate an encounter. That's the whole point of advancing in level and obtaining those new abilities. But you (the DM) should also be factoring in those new abilities into your encounter design, just like you factor in the party composition, party level (vs CR) number of people in the party and so forth into your encounter design.
The tower
I reminded of the old story of a DM who designed a tower adventure for mid level PCs, that was supposed to take a few sessions. Each level of the tower contained fearsome guardians with the top level containing the BBEG. Long story short, the PCs teleported and flew to the top level of the tower, disintegrated their way in and took the BEEG out without dealing with the minions, inside of 30 minutes of play.
The DM was at a loss how to challenge these PCs and the campaign ended.
The issue wasnt the PC's trivialising the encounters; the issue was the DM lacked the experience with PC abilities of that level, and designed his adventure as if they were 1st level PCs. He failed to take into account the abilities possessed by PCs of that level. He failed again, by quitting the campaign, and failing to gain experience DMing PCs of that level.
If I have an entire party of flying PCs (and my last campaign featured just that from mid level to 20th+) and they're trivialising encounters,
you're designing your encounters wrong. You should have a mix of encounters, with decent ranged attacks or spells, flying creatures, encounters set in dungeons where flight is nullified etc, in addition to encounters that are deliberately placed to highlight the PC's ability to fly (encounters where the PCs are supposed to win, or gain a dominant tactical advantage over the monsters on account of their ability to fly).
Past CR 5 or so, many monsters fly. Chimera, Wyverns, Dragons, Sphynx, many Demons and Devils etc. If they dont fly, they have spellcasting or similar traits that also make them able to fly, or alternatively not care if you do. (breath weapons etc). For the monsters that dont fly, have them attack in ruins or dungeons where flight isnt an issue.
Flight is a non issue in 5E. I've had 1st level PCs able to fly and it trivialises nothing.