In the Transformers: Prime/aligned continuity, like the live-action movie continuity, Bumblebee's voice box was crushed by Megatron. Because Ratchet was unable to repair it, Bumblebee speaks in beeps and whistles that the other Transformers can understand, but humans cannot - except for Raf.
Early in the show, there were rumors/theories that Raf was some sort of techno-organic humanoid similar to Sari of TF: Animated, as no concrete information about his parents had been divulged. This theory was effectively debunked later in the series.
There are a few points in the show that Raf comments that he doesn't understand why he's able to understand Bumblebee, just that he can.
Has this ability been explained in any of the other materials (comics, books, commentary, etc)?