As someone who tries to be an empathetic human being, I've come to realize that there are countless things that I do everyday that are not part of any conscious decision making. The way I exist in the world was largely chosen by someone else. If you can acknowledge and accept this, I think it becomes a lot easier to accept people who do not conform to what you believe to be standard operating procedure.
The most obvious of these constructs is religion. Sure, you will meet people who have converted or changed religions for one reason or another (often marriage), but for the most part, no one chooses their religion. You are born into a family, and you accept what they believe. You did not choose it. If you didn't choose it, how can you be so sure that you've got the "right" religion? Obviously, you can't be sure, and that's why it's called faith, but my point is more that you had no part in choosing this. You were not offered alternatives, or the option to forgo religion entirely.
Society has countless social contracts that are completely arbitrary. I mean, why do boys wear pants and girls wear dresses? There is no universe where you could objectively convince me that a skirt isn't more comfortable (in warmer climates). But if I start wearing a skirt, you'll immediately identify me as weird or make assumptions about my sexuality. Did you choose these standards? Of course not. When you were a kid, someone gave you dolls or toy trucks because of your gender. There is no logical reason for this, it's just a standard that you accept, but did not choose.
Gender profiling, of course, is just the start of it. We do the same thing with race, ethnicity, religion, wealth, sexual identity, etc. Many of these social contracts are the source of inequality as we know it today.
So what do you do with this? If you encounter someone or something that varies from your expectation, ask yourself where the expectation came from. If it is arbitrary, and not something you got to choose, maybe it's not something to judge others by. Your system of beliefs and values may not entirely be your own, and they may run counter to the very morality that you claim to embrace.