Doors locks stop working when the transmission is shifted into drive

Do you mean they don't lock if you use the button or key (manual) or that they don't lock when you shift into drive or are in motion (auto-locking)? The auto-locking is something that you can program in most cars. However, Toyota decided that they don't trust the owners and instead require a scan tool to access those settings on your car. Other door lock settings can also be altered using the scan tool.

How much will it cost to have it programed?

That would depend on where you take it. Some shops have scan tools that can do it and would likely charge less than a dealer but it all depends on where you are and what they charge for labor. I know around my area it would be a flat charge at the minimum half hour so about $50.00. Was it locking before this? If so what changed between then and now?