I've only seen this on third party booking sites like Expedia. I've never seen it when booking through the hotel directly, which is usually cheaper. In the rare case where it's more expensive, they'll almost always match an online price if you call, as it avoids them having to pay a commission to a third party.
I've also never seen this happen on Costco Travel, which I sometime use because they have good deals and 2% cash back for Costco executive members (which is in addition to any credit card cash back). Costco focus on quality over quantity - they list a small number of good hotels rather than a large number of average ones.
Something strange in this article is that they didn't include the price of booking directly through the hotel in the comparisons.