As is revealed in [Episode 8 - "Desperate Souls"][1]:

> [Rumpelstiltskin] returns home and uses his power to save his son from the Duke's men. Baelfire [his son] is terrified of this man who no longer seems like his father at all.

It's a fairly safe bet (until the next twist from the writers!) that Rumpelstiltskin's fixation with children comes from the loss (by virtue of fear) of his son when he takes the Dark One's powers.

  [1]: https://en.wikipedia.org/wiki/Desperate_Souls