Bulls strength and conditioning coach Hans Straub said in a since-deleted tweet after the 49ers took Lynch in the fifth round of the draft Saturday: "Thought an organization with 5 Super Bowl titles would have a stricter draft criteria. Clearly, integrity & character are not a priority."
USF announced the resignation Tuesday.
"USF Athletics has high expectations for each and every student-athlete, coach and staff member," athletic director Mark Harlan said in a statement. "To that end, I have accepted the resignation of Hans Straub from the position of head strength and conditioning coach. I thank him for his contributions to USF Athletics and wish him well in his future endeavors. A national search for his replacement will begin immediately."
USF head coach Willie Taggart told local reporters Tuesday that he was disappointed in Straub's tweet.
Lynch, who transferred to South Florida from Notre Dame, was considered highly talented by NFL scouts but does come with some character concerns, which the 49ers acknowledged after drafting him.
The 49ers felt good about drafting Lynch in part because Taggart vouched for him. Taggart and 49ers coach Jim Harbaugh are close friends, and 49ers general manager Trent Baalke met extensively with Lynch during the player's recent visit with the team.
"He believes that this is a good young man," Harbaugh said of Taggart on Saturday night. "[Lynch] needs direction. He needs good structure around him where he's got guys, men that he would look up to, that he would have a chance to emulate. Feels that he'll thrive in that kind of environment."
In a conference call with Bay Area media Saturday, Lynch conceded he has had some issues.
"Regular mistakes a person at my age makes," he said. "Just most mistakes that most people my age make. They weren't mistakes like robbing, things like that. But they're mistakes that weren't supposed to happen associated with football, and I chose to do those things, so those things hurt me in the end. But I'm just happy that my opportunity is finally -- I've been waiting my whole life to be drafted."