Father Gabriel clearly opposes Negan’s methods, but he’s not one to physically rebel, which offers little room for any secretive pretext.
One of those personalities obviously fits Simon’s best interests far better than the other., even if the flu-esque Father Gabriel might be clandestinely heading to the Hilltop Colony soon.
Meanwhile, Eugene is a Yes Man on all fronts, which casts doubt on all of his motivations.
Simon doesn’t share Eugene’s distinct smarts, but he’s by no means an idiot, which makes him rightfully suspicious of the way the stressed-out redneck has carried himself since he was taken from Alexandria.