Mashiach Agent – there are so many qualifications to the Mitzvah of tochacha anyhow, so a lot of the time it’s not relevant (although of course, there are times when it is).
But you do have a valid question for those situations when it does apply.
1. Being dan l’kaf zchus doesn’t apply in every situation. I can’t look up the halachos this second, but for example, if you know that someone isn’t frum and always drives on Shabbos, you do not have to assume that they are having a baby every time they drive on Shabbos. On the other hand, if you see your frum neighbor in a car on Shabbos, you should definitely assume that she is having a baby or has some other emergency.
2. Even when you give tochacha, you can be dan l’kaf zchus simultaneously. If you see someone cutting in line and you feel that it’s appropriate to give him tochacha in this situation (which you should think carefully about, because it’s not always the right thing to do), you have to think carefully about how you give tochacha. You need to give it in a pleasant way and you can say it in a way that leaves open the possibility that he had a reason for cutting in line.
And honestly, maybe you should not be giving tochacha in that situation. Maybe you should be assuming that he had a good reason. It is perfectly possible. Maybe he was really in line first, but for some reason the cashier told him to take care of something and come right back. Or maybe he had an emergency. There can definitely be many reasons why it may appear that someone is cutting and he really isn’t. Also, sometimes, people really don’t realize that someone is behind them or they are not sure where the line is.