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Amy was kidnapped because she was pregnant with a child (later named Melody Pond &, later still, also named River Song) who'd been conceived in the TARDIS, while travelling through the spacetime vortex. As stated in "A Good Man Goes to War", it was exposure to the vortex over many generations that originally gave the Time Lords some of their abilities, including regeneration. Although Amy's child was nowhere near being a Time Lord, she did have the beginnings of Time-Lord-like abilities.

The Silence decided to enhance the child's abilities by manipulating her while still in the womb, in order to turn her into a weapon against the Doctor. Since the womb concerned was inside Amy, the Silence needed to kidnap Amy to get at her unborn child.