Sorry, but I am going to both agree and totally disagree with that simplistic view. For a simple business, or maybe you could even say for "many" self-employed business owners, sure it can be simple and have only one way of doing things. They collect their pile of receipts, books, etc..and so forth, hand it over to the CPA. And its so easy to do that, I don't know why they just don't do it themselves with Turbotax home and business edition. Its not hard as you said.
On the other hand, a top sophisticated and clever CPA can work with a more sophisticated business owner to do things in ways that are extremely complex. I know people who started their own small business, have only 1-2 employees, and the taxes they do are incredibly complex the way they handle everything .. They also setup LLC's and other complex structures to meet the unique needs of that business. And again, I am not talking about a large corporation, just a single owner ..
So Yes .. there are so many many different ways to set up a small business and manage the income,expenses, and so forth ... It can be very simple as you said, to extremely complex and mind blowing with techniques that I can promise you that you never heard of (I didn't until this guy explained me all the things they are doing) ...
Going back to this OP, we have no idea whether he has just a simple business or a complex setup that his CPA did ..
But ok, I admit, this sounds like something very simple .. and I bet we don't have all the facts and truth's about what both the CPAs really said and whats really going on ... So all our speculating is just making a huge set of assumptions .. But I bet this is all about him trying to manipulate things to qualify ;...