This is absolutely false. Not every car is offered with manual transmission, but cars that can be configured with both are almost always cheaper with a manual. I cannot recall every seeing a case where it was the more expensive option.
My girlfriend's car got stolen a few years back. When I asked the cop how much this happens locally he asked me what I drive, and when he found out my car had a manual transmission he laughed and said nobody would steal my car - the kinds of people who steal mass market cars don't know how to drive a manual any more.
$800 more with automatic, about 5% of the cost of the car.
If you are lucky the dealer might have a cancelled order on the lot with a manual transmission.
On top of that, automatic transmission cars are more fuel efficient, so the operating costs might be a wee bit lower.
Manual are cheaper and ubiquitous. If you want an automatic car in Europe, you pay premium on a new car, and a very large premium each time you rent a car.
I'm not sure how that works for second hand cars - there are less but less people interested too, so not sure where the balance tip. In any case, automatic car tend to be expensive cars to begin with (BMW Series 5, ...) - you won't find as easily a regular joe car that is automatic.