In discrete memoryless channels what is meant by output probabilities?
The physical significance of the the output signal is that it's the thing the receiver can actually observe.
The whole point of a communication system is to convey information about something the receiver can't directly observe (the input signal) through some channel to a receiver. If the receiver already knew the input signal they wouldn't need the communication system, they'd simply act on the information they already had.
If we observe the output of a communication system for some time, we can use statistics to estimate (with some uncertainty) the probabilities of receiving different messages. We only know what messages were sent at the transmitter by using our observations of the output signal and the math you're learning now to estimate them.