I think just in terms of general GMing philosophy, when you start thinking along the lines of "how can I make X character ability useless?" you have gone down the wrong path. I've seen it with flight, sneak attacks, eldritch blast, high stealth checks, divine smite, etc.
Your job as the GM is to make a fun experience for everyone (sometimes that includes making things a tough challenge, sometimes it doesn't) and making it so a core PC ability is useless at best and suicidal at worst makes a lot of players feel like you're trying to send a message to them that they shouldn't play certain types of PC. Generally-speaking, the earlier in a character's class progression an ability shows up, the more they should be able to rely on it.
A better way to look at adventure design, IMHO, is to say "with a character that can do X in the party, what kinds of scenarios can I construct to make things interesting?" For example, let's say that the flying druid finds a place that they'd really like to access, but they can't get in because the lock is too good. Now you need to figure out how to get the rogue up to the peak it's on/across the lava lake/whatever so they can pick the lock you can't touch on the stone doors your strongest wild shape can't break down.
You'd have never seen the thing if you couldn't wild shape, but you still can't solve the problem alone.
Or maybe you do spot some hostile forces ahead of time. Like, a LOT. More than you can just handle with an ambush. Now everyone needs to help make a plan. Are you going to make some temporary fortifications? Find another way around? Try to sneak past? It doesn't matter what they choose, the druid gets to feel cool for keeping the party and those they are protecting from stumbling into a massacre and now they have an interesting decision to make.