I once had a position where my Knight and Bishop drove a king away from protecting his Rook. I guess this shows the Rook's weakness?
Bishop and knight trade for rook?

I also think the two pieces are better and stockfish also said that.
But i remember gothamchess 2 or 3 Times saying, the rook is better

gotham never said that, infact he said the opposite. but still thats dumb cause its obviously better

The computer used it against me in hard mode,
After 17 years, it is almost impossible to figure out what this means. Does anyone recall ever being "hard mode" on chess.com?

Clearly every exchange is contingent on the position. If the rook is threatening mate or the win of material you may be forced into this exchange. On the other hand if when the dust settles one side has a bad bishop and a knight trapped on the rim of the board removing the active rook may be a very favorable exchange. That said the 3 3 5 valuation is easy to remember but a more accurate measure is Bishops 3.25 Knights 3.17 Rooks 5 (Queen 8.17, this is why 3 pieces are generally better than a Queen). So given the exchange mentioned in your original post you would give up 6.42 to 5 even if you add a pawn to the mix to would be 6.42 to 6. If the exchange is at f2 or f7 you probably gave up an active Knight and Bishop for an inactive Rook maybe adding as much value as 1 pawn or 7.42 to 6. Another way to look at this is take a rook and place it anywhere on the board it can effect 14 squares a bishop 13 ( in the middle of the board) a knight 8 (again in the middle) 21 is greater than 14 if the add 2 for the pawn again the BN is much stronger.

Openings and middlegames: bishop + knight > rook (+1-2 pawns)
(unless if the bishop and knight are extremely passive and blockaded by your pieces)
Endgame: Rooks become a bit more powerful, unless if there are many pawn chains in the position
It really depends, but in my opinion, 70% of the time a bishop + knight > rook (+1-2 pawns)
You gain 1 point in material