In order to USB the USB pins as normal GPIO pins you need to set iomode bit in the USB_USBIO_CR1 register. Please refer to the PSoC 5LP register TRM for more details on the register (see section 1.3.564)
The I/O mode bit in the USBIO_CR1 register puts the USB in either USB mode or Drive mode. When put in Drive mode, the USB signals are disabled and the bits DMI and DPI are used to drive D- and D+, respectively. There are two different drive modes. In CMOS Drive mode, D+ follows the DPI and D- follows the DMI. In the case of Open Drain mode, the pull up resistors play a role. In this state, when the DPI and DMI bits are set to high, D+ and D- are high impedance (Refer section 24.5 of the PSoC 5LP Architecture TRM)
Did you make the above change?
I have created a small project that can be tested on the CY8CKIT-050 in which I have used the USB pin as an input pin. When supplied with a 1 on the input pin the LED stops blinking.