To automatically boot, you need to change the settings in the kernel:
- In the NIOS II IDE, select Configure Kernel for the kernel project.
- Select Device Drivers -> Character devices -> Serial drivers
- Turn off the Altera JTAG UART Support
If you want the console on the RS-232 port, you can select the NIOS serial port and Support for console on NIOS UART options.
Exit and save the new kernel configuration, then rebuild and upload.
You can leave the JTAG component in the SOPC builder, so that you don't need to recompile in Quartus when you need to re-enable JTAG.
Tony