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Ah, good question! You measure throughput pretty much as you think what's best to represent what's meaningful to you.
For example, if you have Ethernet, it's transmission rate is 10 Mbps, but we have L2 (Ethernet) overhead, L3 (e.g. IP) overhead, often L4 (e.g. TCP) overhead, often higher protocol levels (e.g. FTP, NFS, CIFS, etc.) of overhead. Then we also often have data loss on networks, so we have also often have retransmission overhead.
Consider ASCII text. Perhaps for that, you'll want to measure throughput at CPS (characters) per second. Which is fine, but is your ASCII text 7 bits or 8 bits per character? 7 bit character CPS may be faster than 8 bit character on the same medium. If you have a higher level protocol that's doing compression and/or caching, your effective transmission rate will be even higher.
Because of the complexity caused by all the above, in networking, we often just measure percentage utilization of the medium regardless of other considerations. It must be understood, that's just to avoid dealing with the above, yet sometimes we need to. Even something as minor as tagged vs. untagged Ethernet frames will impact effective data throughput.
