Headlines can be difficult to understand because they are sometimes purposefully misleading or have double meanings to try to get you interested enough to read the article.
Question as a verb with an object can mean either '1. Ask (someone) questions, especially in an official context' or '1.1 Feel or express doubt about; raise objections to'.
After reading the article, Commerce Minister Nirmala didn't actually ask any questions, she just pointed out the hypocrisy of developed nations trying to say India is protectionist when they are acting in ways that are just as protectionist.
It seems very clear to me that "questions" in this sense is being used to mean "objects to", but the headline doesn't make it clear because it omits what the rich countries did that Nirmala objected to so that the headline isn't too long. If I question you, I interrogate you. If I want to object to something you've done, I question your actions, not you.
I suppose I could doubt your existence, but I still wouldn't say "I question you", I would say "I question your existence.". I could say "Don't question me - I know what I'm doing!", and I would be using that somewhat in the sense of "don't doubt me", but I'm not certain. I have to think about that case a little more. I think I would be more likely to say "Don't question my methods!" though.
Here are two example sentences from yourdictionary.com that show the difference:
Every Friday they went to town for groceries and he never questioned what she bought.
Everyone was pleased to see Pierre, everyone wished to meet him, and everyone questioned him about what he had seen.