SF's pass defense is terrible but some other things to consider to put things into a finer context.
BROWNS INJURED WR CORPS
Browns WR corps has been devastated by injury. They were without WR Andrew Hawkins and WR Taylor Gabriel yesterday and had to activate practice squad WR Dareus Jennings who made his first NFL appearance in a regular season game but then they lost WR Travis Benjamin who was the only deep threat on the team AND they lost WR Marlin Moore. Oh and late in the game WR Brian Hartline also got hurt leaving Dareus Jennings as the ONLY HEALTHY WR on the team at one point (Hartline limped back into the game in the 4th quarter).
Hartline is hurting and probably isn't 100%. Benjamin might not play Sunday and if he does he may not be 100%. The coaches have only played WR Dwayne Bowe in one game but they might have to use him and they just re-signed WR Terrell Pryor but didn't activate him yesterday preffering to have 28 defenders to only 18 offensive players active which is mind boggling but back to point.
UPDATES:
Scott Petrak ct @ScottPetrak 21s21 seconds ago
#Browns CBs Joe Haden, Justin Gilbert and
WRs Andrew Hawkins, Taylor Gabriel remain in concussion protocol
Mary Kay Cabot @MaryKayCabot 56s56 seconds ago
#Browns WR Moore X-rays on ribs negative; WR Benjamin (shoulder) day to day; FB Malcolm Johnson (groin) could be serious
BROWNS TERRIBLE RUSHING ATTACK
The Browns also have the worst rushing attack in the league. They just don't run and when they do they are just bad.
BROWNS TERRIBLE DEFENSE
The defense sucks. The ONE WIN that Manziel had came against rookie QB Marcus Mariota who was making his 2nd NFL start and he looked bad. It was the only game the Browns defense actually had a pass rush. I don't think Blaine Gabbert is much better so that should work in favor of the defense.
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I don't see how the coaches can sit Dwayne Bowe. He 'should' be an improvement over smurph WRs Hawkins and Gabriel. That could benefit Manziel. The running game got 'somewhat' untracked yesterday with Crow so that should also help. Playing at home against the Niners who come east for the second week in a row helps. The defense facing Blaine Gabbert, one of the worst QBs they've faced, should also help Manziel.
So for as many issues starting against SF is the perfect storm for Johnny outside of losing starting OG Joel Bitonio many things work in his favor.
If he continues to start after Sunday then the sledding gets much harder facing, @SEA, @KC, and PIT. So nothing gets decided no matter how he performs Sunday.