There are some situations where the business owners are correct, especially if their competitors are permitted to tack on extra fees at checkout. Sometimes it is necessary to establish a global rule to prevent prisoner's-dilemma defections.
Below the line fees are a political statement, and act as political back pressure against the purported source of some costs.
Two, customers (yes, that's us I'm talking about) are dumb and superstitious when it comes to numbers.
$10 = oh no, that's bad
$9.99 = oh, that's perfectly fine!
By raising 'visible' prices for everyone some portion of the customers will shy away from the product, say by buying groceries rather than eating out.
Respecting the agency of customers to make informed decisions for themselves. How terrible.