What's the real difference between throughput and capacity of a network cable?
"Capacity", similar to many other terms, is a an overloaded word. In the example you bring, it seems that the meaning is equivalent to "throughput", i.e., the maximal "amount" of information a channel/network/etc. can transfer per time unit. 

However, while these terms can be used interchangeably, to my ears "capacity" has the feel of a theoretical limit, while "throughput" has a feel of a practical limit. As in: "the capacity of a fiber channel is 1Gb/sec, which (due to coding, errors, and technical limitation)  leads to a maximal throughput of 986KB/sec (=of YOUR data)". 

A different explanation which may be used in other settings is a one in which the capacity of a link is measured in relative terms, that is, it will be a ratio between 0 and 1, to be multiplied with a predefined  maximal rate of information transfer. This notation is useful when computing flows over the network.