The Raspberry Pi uses 3.3V level for it's UART, like most Flight Controllers available today (including but not limited to: pixhawk v1, Cube black, Cube orange, Matek FC, holybro FC) while Micro controllers such as the Arduino use 5V. Directly connecting these to the Raspberry Pi will ensure membership of the aforementioned club. As with most issues there are two ways around this, a nice way and a cheap and easy way.