FlashProgrammer has some problem!

If you jtag uart, then you must have nios2 terminal connected.

NOTE, you can use JTAG UART console during development. But if you don't connect a nios2-terminal, the program will hang. So you shouldn't use JTAG UART console for standalone or production. You must disable JTAG UARTconsole then. You still need a console device after disabling JTAG UART console, otherwise the init task will exit and panic. You may use Nios serial uart as console, or use Virtual Terminal (actually it can be dummy) as console.

If you use serial uart, you use RS232 cable with hyper-terminal on Window, or minicom and kermit on Linux.