You're correct. "How come" usually carries a complaining tone. It is better to say "why."

I don't think that 'How come?' necessarily suggests that you are complaining. It all depends on the subject, and on your manner or tone of voice. 'How come?' is simply an informal way of asking for an explanation.

I think in a situation where a direct "why" could sound abrupt or demanding, "how come" is received better by the listener. For example:- The boss asks the employee: " Why wasn't this work done yesterday?". The employee asks the boss: "How come I didn't get a raise this year?". Of course I am not suggesting that you give such cheeky replies to your boss :) The two examples are not those of a contiguous conversation.

No saying "how come" in asking a question doesn't sound like ur complaining basically "how come" is used in the sentence where it's telling the receiver of the message that your curious instead