Cheever is astonished because he never thought the Proctors were capable of such diabolical evil. He'd always trusted them implicitly. But now that he's been presented with what he sees as hard evidence of their involvement in witchcraft, he's absolutely petrified. He knows what happened to Abigail Williams at dinner that night: how she doubled up in excruciating pain, screaming that she'd been stabbed in the belly. Now that Cheever's seen the poppet with the long needle sticking through it, he immediately makes the connection and is now convinced that Elizabeth Proctor is a witch.
Naturally, Cheever's worried that what happened to Abby could just as easily happen to him. Like everyone else in town, he's utterly convinced that there are dark, malevolent forces at work, which could strike him down with death or illness at any moment.
Cheever has not once doubted the Proctors. He did not believe Abigail's story that Elizabeth's spirit stabbed her in the stomach. When he finds the poppet, he is astonished, not because he thinks that Abigail has planted it, but because it is evidence enough for him to believe that Abigail was telling the truth and Elizabeth is a witch. He is afraid both by the thought of what will happen to her and the thought of how rampant the witchcraft is in his own town. Cheever is blinded by the town consciousness and is unable to assert his own identity and wisdom into the situation.