Let's not forget that it was Toby's house that exploded a few weeks ago. Could that have been a first attempt made by "A"?
"A" has been known to target the police, with victims like Detective Wilden and Garrett Reynolds.
Why He Might Be Safe:
Toby's been on the "A" side before and already eluded the clutches of "A" once. He's smart.
"A" has proven at this point that Toby isn't really a threat. He's not causing trouble, and he's not directly involved in anything in Ali's disappearance. At least that we know of.