I loaded the FLIRC software and configured the minimalistic buttons with Tivo Remote and plugged it on Nexus Player(with otg cable) and it doesn't navigate.

Am I missing something here?  Do i have to somehow pair the FLIRC as a Bluetooth with Nexus player? Does FLIRC support Nexus Player?

Flirc has nothing to do with Bluetooth.

Do you have USB debugging turned on? If yes then you need to turn it off for OTG to work.

You can also test if OTG works properly by connecting a standard USB keyboard to your Nexus Player and check if you can control it with the keys on the keyboard. Flirc acts as a keyboard so if a real one can control the device then Flirc should also work.