Where the niners defense is weak is in long passing plays.
However, the strength of the niners is the pass rush to prevent long passing plays to be developed.
So QBs end up checking down which is where the niners secondary is positioned.
The LBs and CBs are programmed to go downhill on the first break of a short route.
Because they expect that the QB won't have enough time for a secondary or an option route to be developed.
Teams that do well are the ones that can stretch the niner defense.. but that comes first with good pass protection or a mobile QB.
Case in Point, the Seahawks owned the niners when Russell Wilson was QB. Seattle didn't have a good OL, but Russell's scrambles and then his penchant for chucking the ball down field and accurately, basically plays well against the Niner defense.
Teams left that match up better against Niners D:
1) Eagles: Hurts can scramble a bit, and tends to throw more of the intermediate depth passes. OL is pretty good as well.
2) Chiefs: This year's Chief doesn't match up well due to not having Hill to stretch the defense. Mahomes has been more of a check down passer this year especially with Kelce as his main option. A mobile Mahomes will help.. a high ankle sprain Mahomes... really hurts alot.
3) Bengals: Can really argue to put Bengals in the #1 slot because of gunsligning Burrows and his WRs, but their OL is banged up bad. I don't think Burrows will have any time.