Short Version
A fragment pipeline refers to a pixel shader processing pipeline. Note that this is not the same as a 'pixel pipeline', it is simply one portion of a pixel pipeline.
Does It Matter?
Yes, definitely. The number of fragment pipelines has a direct correlation to the performance of a given card.
Long Version
These days the name of the game is processing pixel shader programs. Pixel shader programs are what produce all the cool effects in modern video games, like lens flares, light blooms, and heat distortions. Since these programs have to run for every single pixel on the screen, it stands to reason that more of them means faster rendering.