Music notation conventions have changed, at different times in history.
Bach did not give any tempo indication for the prelude and wrote it in common time. Therefore the written "beat" was a quarter note, i.e. every four written notes.
In Bach's time, musical tempos were defined relative to the human heart beat, not as MM values (the metronome had not yet been invented). Some contemporary books on music theory compared the pulse rate with the length of a swinging pendulum, which gives the default tempo at that time (and the average heartbeat rate of musicians!) as about 80 beats per minute. The practical range of tempi varied from two musical beats in three heartbeats (i.e. about 54 BPM) to three musical beats in two heartbeats (i.e. about 120 BPM).
Modern dance music tends to use faster tempi but with fewer subdivisions, so your instinct to count 2 notes to a beat and not 4 is probably not too far from the historically "correct" performance speed. But a classical musician would probably "feel" the rhythm of this piece with only two (slow) or one (very slow) beats in each bar - i.e. the "beats" correspond to the "chord changes" in the music, not to some faster rhythm.
In music of Bach's time, the shortest written notes in different pieces tended to be of similar duration, independent of the tempo in "beats per minute." Thus, "slow" pieces (in terms of BPM) were often written in shorter note values than "fast" pieces. In the absence of precise tempo markings (no metronomes!) this was a useful visual clue as to the character of the music - the score of a "slow" piece would typically have lots of 16th and 32nd notes, while a "fast" one would be written mostly in quarters and 8ths.