what is transparent operation on rf?
From this document:


  "When operating in transparent mode, the modules act as a serial line replacement."


It means that the RF module hides the implementation of the transmission protocol from the user. Xbee for instance may use the Zigbee protocol, but appear to the microcontroller as a simple UART.



To the user the cloud just hides the wire, while in reality it may hide any level of complexity, in this case a wireless Zigbee connection, including everything required to run the protocol:  



The "why" is obvious: the designer doesn't have to bother about the communication protocol, and just send and receive UART data as if his microcontroller were directly connected to the other controller.


  So, "Transparent operation" means hiding certain implementation details from the user, so that the system is easier to work with, yet with the same user functionality.


edit about drawbacks
Like Kellen already said one drawback may be cost, especially if you work at short range. (A kilometer wiring also costs money). Noise is not a problem if your RF modules are FCC or CE certified. RF even has the advantage that you have electrical isolation, which also may prevent noise issues.