I've been looking at a bunch of flight schools the past year (and haven't picked a single one, which is due to various reasons, especially Covid) and I've seen both good and terrible ATOs. Now, I wouldn't call it "fear" but here's what I pay most attention to:
Cost
Cost is obviously a big issue. Flying is expensive and I know that - nothing new here. However, there are multiple things to consider, these are things which I will usually ask the very first day I take a look at an ATO. The first thing is the way you pay for the training. If you have to pay everything at once (quite common for Integrated courses), then that's a major red flag. ATOs know that some people are simply not made to fly airplanes, so if you pay everything at once and possibly get a loan from a bank, just to find out that you don't like flying, you're in big trouble. I would never ever pay all the money up front, even if I love everything else, like the facility, the people, the airplanes and whatever else there is.
Something much better is either steps (so you pay for your ground school, then PPL, then CPL/IR etc.) or even just paying as you go, so essentially you pay for every flight hour you take. Both options are far better than paying everything at once.
Not only do I care about the cost of the course itself, but also about what's included. What about additional hours that you possibly need? What about material like books, question banks, your headset, uniform and all that stuff? I know, those aren't that expensive but they still cost money and if you drop 80k on a course, you might as well get some books out of it. If not, then that's not necessarily a red flag but kind of weird because I'd expect a flight school to provide me with necessary material to complete the course.
Facility
The facility is probably one of the most important things to me. While cost is a major thing to consider, there are plenty of schools that offer good ways of financing your training, so once I've picked out a few ATOs that do this the correct way, I'm going to look at the facility. This is basically just to see how much the ATO has invested to make sure that they provide a good product. I've seen very small ATOs that take you to bigger simulators during your flight training and I've seen ATOs that have simulators right at their own facility. Both options are fine, however you need to consider travel cost to those simulators as well as the amount of time it takes to get hours on them. In the end, those simulators are probably located at a different ATO, which means that you have at least 2 ATOs that use the same simulator(s). This can be a massive bottleneck.
Then there is also the school itself. And while this isn't the biggest "fear" or anything, I just like to take a look at the rooms, the school itself and the campus. I've seen some that just look terrible and while yes, this doesn't necessarily mean that the ATO is bad, it still gives you a first glance at what to expect.
Planes are also something to look at. Does the ATO actually own them? How many students are there and how many planes are there? Do they even work? How old are they and what type are you flying? In the end you'll spend a lot of time in airplanes, so you should feel comfortable flying them. There are ATOs that share airplanes with private people or other ATOs, which could possibly mean that it's hard to get hours - again something to consider, since you need your hours, usually ASAP to get your training done and start flying for money.
History
I've seen so many people rush into a random ATO, just to find out that it was a terrible mistake and it's about to go bankrupt. Then they have a massive loan, no license, no future and their dream is over.
Look at your ATO. Take a look at the past, take a look at weird rumors (they don't always have to be true but research is always a good idea), see how it's possibly tied to other businesses or even airlines in very rare cases. Has the ATO been around for a while or is it a new one? Has there been one before that failed or went bankrupt? This does happen. And I know people that fell for it.
Last but not least, and this is more about the present than the past, what do they offer and does it sound too good to be true? If yes, then it probably is. They don't give out presents. ATOs aren't charity projects, they want money.. from you. So be careful with them. I know some that will tell you stuff that sounds great, some will help you get scholarships and all that stuff and while those things might exist on very rare and special occasions, there are far more ATOs that will tell you about it, than actually offer it.
In the end it's all about research. Out of all the ATOs that I've researched and visited, there's not even a hand full that I'd actually take. In fact, in the DACH (Germany, Austria and Switzerland) area there are exactly three ATOs that I'd even consider - and one of them is far too expensive for me, so it's actually two. Two out of at least twenty that I've looked at. And I'm still not taking a single one of those. Because it's too risky.