First, I'll address the nature of the Triforce. It isn't distributed on the whim of the goddesses. It's an inanimate object that follows whatever rules govern it. So when the ToP is sent to Ganondorf, there is no "why would anyone do that?" There's no conscious decision. It just happens. It's ultimately caused by the forces of balance described both in OoT, referring to the three aspects of the Triforce, and in TP and SS, referring to good and evil.
Most of the people here are saying it's destiny at work. That's only partly true. What literally happens is described in the HH:
Link has the ToC when he starts the CT. From WW, we know that the ToC is split on the AT when he leaves, so he must have the CT version of it. i.e. the whole Triforce exists on the AT (ToW with Zelda, ToP sealed with Ganondorf, ToC split and scattered), and the whole Triforce exists on the CT. CT-Link has the CT-ToC. "the Triforce remained with the chosen ones of the Gods." (Other statements regarding balance, as I mentioned earlier, also support this.) Therefore CT-Zelda receives the CT-ToW and CT-Ganondorf receives the CT-ToP.