There's nothing wrong with a Kubota, but they are no better than any other quality diesel engine.
Other manufacturer's use them because they can get them for a great price when bought in bulk, and Kubota is willing to deal. It saves the buyer money, and Kubota is still making theirs as well. It's simply a matter of win/win for both parties. It has little to do with whether Kubota engines are the best.
Most companies who have to source parts of any kind from another manufacturer try to buy something that won't hurt their reputation, but the bottom line is always cost, and the best is usually not the cheapest. If Kubota's were actually the best, they'd also be the most expensive either individually, or in bulk.
They are a good engine at a good price (from a manufacturer's standpoint). On top of that they have a good distribution system here in the USA that allows them the luxury of making bulk deals to companies here. Yanmar doesn't have anything close to that type of setup here.
Finally, the Kubota name is much more recognizable to most folks than the Yanmar name simply because of all the Kubota tractor that folks see all over the place. Very few actually know that when they are looking at an equal number (actually more) of Deere tractors, they are looking at Yanmar engines (at least up until the 4000 twenty series of compact utility tractors came out).