FPGAs are awesome — they can be essentially configured into becoming any computing device you want. Simply load your selected bitstream into the device on boot, and it behaves like a different piece of hardware. With great power comes great responsibility.
You might try to hack a given FPGA system by getting between the EEPROM that stores the bitstream and the FPGA during bootup, but FPGA manufacturers are a step ahead of you. Xilinx 7 series FPGAs have an onboard encryption and signing engine, and facilities for storing a secret key. Once the security bit is set, bitstreams coming in have to be encrypted to protect from eavesdropping, and HMAC-signed to assure that they are authentic. You can’t simply read the bitstream in transit or inject your own.