Is the pharmacist asking me why I am taking a certain
Medication a hipaa violation?

My pharmacist takes even better care of me than my doctor does and knows as much or more about drugs and interactions with foods and other drugs. He makes sure I understand the med and dosage, etc . Many meds are taken for more than one reason, so I would think it is a good thing that your pharmacist knows what is going on with you medically. If he has questions and maybe reservations about the prescription, he should talk with the prescribing doctor.

No its not. It's the pharmacist's job to understand why you may be taking a medication to judge whether there might be a problem. By asking the question the pharmacist is asking your permission to have the knowledge, you can refuse and say you trust your doctor.

This doesn't even come close to a HIPAA violation.

A doctor knows a lot of what is going on in your body, as does a pharmacist. A pharmacist often knows the medication and the resulting effects better than a doctor because that is their job. They will often pick up possible negative drug interactions between all your medication that your doctor will have overlooked.

He's looking out for you and your health. This isn't a HPIAA violation.

In addition, it never hurts to have checks and balances, because doctors can and do make mistakes in all sorts of ways:
Name of one drug very much like the name of another
Limits of maximum dosage may be exceeded
Interactions with other drugs you take, especially from another doctor
Your history, a condition that is a warning to avoid this drug

I have had one or more happen. Each of my parents did. The news of full of such stories. It's rampant. People die.
I would thank your pharmacist for asking.

No violation - good and thorough service. You don't have to answer the question but it's best if your pharamacist does get his questions answered. There may be instructions related to the drug that are specific to your medical circumstances.