I have a dispute with a company that has not refunded my charges since I returned their product, so I decided to file a dispute agains them with Amex. Does this look bad when Amex looks at me as a customer? Are there any negatives to doing this?
I'm assuming you went through the company's return process correctly, and have given them notification and enough time to properly respond to your request to return your money.
If this is the case, it shouldn't look bad for you as the customer. It's called a chargeback in most cases, and it looks bad for the merchant. Typically American Express is excellent when it comes to disputing charges, in the event of return, theft of card, etc.