Bautista aggravated his throwing arm during Tuesday's series opener against Baltimore following a series of events that unfolded after Orioles reliever Jason Garcia threw a pitch behind the back of Toronto's All-Star outfielder.
Bautista, who has a history of hostilities with Baltimore pitchers, responded later in the at-bat by blasting a home run and drawing the ire of several Orioles players with his subsequent celebration.
Garcia and the Orioles denied intentionally throwing at Bautista after the game, but Anthopoulos sounds unconvinced.
"People are going to say the ball slips, and this and that," the Blue Jays GM told MLB Network Radio on Friday. "I'm just sick of Jose Bautista getting thrown behind all the time. It's happened more than once."
Bautista, who was plunked a team-leading nine times last year, has been hit once this season and took a pitch to the head by former Orioles pitcher Jake Arrieta in 2011. Anthopoulos fears Bautista's become target practice for opposing clubs looking to send a message.
"I know players take care of things between themselves and between the lines," he said. "But when it happens repeatedly to your best player it's hard to watch."