It's a good question, certainly. Without a lot of specifics, it's tricky to give a specific answer. But I can see what you mean: an ATC delay leads to a delay in getting a gate ready, there's a delay getting the doors open, you end up missing a connecting flight. The ATC delay on its own wouldn't cause you to miss the flight, but the flapping around does.

Now unsurprisingly if the ATC delay (or whatever) was the principal and overarching cause of the delay you can be very sure the airline will rely on that aspect for refuting the claim. If it's a lot more messy (e.g. a delay in ATC leading to longer delays on other sectors) then at the end of the day that is why we have a court process to sort out disagreements. So if you can identify a clear airline related failure that was the main reason for the delay, then you may be in with a chance, but it's unlikely that an airline will give in too easily.