I am building a program for my FRC team and I have need to have up to six controllers. However, the Open Joystick VI only allows up to 4 USB inputs. Is there a way to increase this number or is it is a limitation of the driver station?
You are limited to 4 joysticks. This year (2014) the Driver Station shows up to six, but that is just to accommodate the TI Launchpad which shows up as two joysticks. You mention six controllers - if you want to control six motors, that you can do.
The standard FRC software uses a type def that defines only 4 joystick values. While it may be possible to modify the type def and use additional joysticks, doing so is an advanced use case that could cause unanticipated problems.
If we know more about the type of input you desire we may be able to work out some better alternatives. For example, if the desired input is binary such as forward and backward, the motion could be mapped to existing joystick buttons or use an xbox controller with thumb pad.