How to upload one program into several Arduinos at once?
Are you programming them for the first time or doing a update?

If is the first programming, I cant see another way. 

Otherwise, If is a update and your Arduino have a Wifi module you could try something like an update on the air, where you put your new firmware in a server for example and all devices updates yourself automatically or by a command.

Google for Arduino OTA (on the air) you will get a lot of source code and examples of doing that.