You need to understand that the point system is only a rough guideline meant to assist you in evaluating positions or in deciding on potential exchanges. Many factors, particularly the pawn structure, influences how valuable pieces are. Rooks tend to be better in open positions with fewer pieces/pawns on the board, bishops can get hindered in closed positions by pawns of the same color ("bad bishop"), etc.
Despite of all this, the 5/3 values for rook/bishop (or the piece valuation system in general) is surprisingly reliable.
A rook is generally more valuable than a bishop because:
- it can reach all squares of the board, while a bishop can stay only on squares of the same color
- it can mate in KR vs K, while you cannot win KB vs K.
- it covers more squares (can always move to 14 squares on an empty board independent on where it is placed, while with a bishop it can vary between 7 (corner) and 13 (center) squares)
The exact values "5" and "3" are basically found from experience and since there is a bit of a drawing margin in chess, the exact values don't really matter.
One notable and very common exception to the rule is found in many (beginner's) opening play where a bishop and knight can be exchanged for a rook + pawn on f2 or f7. In these cases almost always having two light pieces is better even though you exchange 6 pawn units for 6 pawn units.