Speaking as someone that works on cars I can say that there are pros and cons to both. In drag a tuned auto will beat a manual hands down. For every day driving autos tend to give better fuel economy and will work. They are easier to drive, but have several drawbacks. Such as a car with an auto will cost more to buy, they cost more to maintain, assuming you dont burn the clutch on a manual...
On the price: For a new car, a manual, if available, will generally be less expensive. However, for some cars, the manual is offered only on a stripped-down trim level which offers poor value for the money compared to a mid-level trim which provides an assortment of generally desirable goodies for not much extra money. So even though the automatic costs more, choosing it allows you to purchase a car which offers better value, assuming you want the extra features.
Although some family cars like the Honda Accord sedan or the Toyota Camry are, in theory, available with a manual transmission, most dealers do not order them. Accords and Camrys with manual transmissions are like 1-in-10,000. If you wanted one, chances are it would have to be obtained from another dealer, possibly quite far away. (There might not be a manual transmission Accord or Camry available in the entire state of Texas, for example.) You would end out paying more than the cost of an automatic because of the hassle and transportation costs involved for the dealer to obtain the manual vehicle.
On the repair cost issue, on a new car, if the automatic tranmission fails, it will be covered by the drivetrain warranty. If you wear out the clutch, that is a wear and tear item, not covered by warranty.