The main reason is, simply, not that Bxh6 is bad, but that the computer, being so strong sees that many more lines that are crushing for white. After looking at it with a computer, what I saw is that black simply cannot finish development without serious concessions....much more than Bxh6, which did not even make the top 5. That is the answer to the question "Why?"
P.S. One other comment, and I mentioned this in an answer the other day, but it also comes down to "cashing in too early". You have a lot of strong pieces, and black is very unfortunately placed, the Qe7 in particular, and these pieces when working together will win material eventually. Keep your threats, and build the pressure. Learning when to cash in on an advantage, and when to keep up the pressure, is a skill that is not often discussed in chess.
Also, many weaker players, and I am not lumping you in to this since I do not know your level of play, but they tend to see doubled pawns as the end-all-be-all of chess. Some doubled pawns are bad, and some are not. Here, they would not be great, and h6 is lost by force if white wants it, but there is just so much more to be had in this position.
[FEN "rnb1k2r/ppppqppp/4p2n/4P3/2PP4/2PB1N2/P4PPP/R1BQK2R w KQkq - 0 9"]
9. O-O (9. Bxh6 gxh6 10. O-O O-O 11. Qd2 f5 12. exf6 (12. Qxh6 Qg7 {And you still have to win.}) 12... Rxf6 {And you do have a large advantage, but not as much as you could have.}) 9... Nf5 10. a4 {And it is impossible for black to develop effectively.} Na6 {This is best per the computer, but only delays the problems of finishing development.} (10... b6 11. Be4 c6 12. Ba3 {With a winning position.} d6 $2 13. Bxf5 exf5 14. exd6 $18) (10... d6 11. Bxf5 exf5 12. exd6 Qxd6 (12... cxd6 13. Re1 Be6 14. d5 $18) 13. Ba3 $18 {And Re1 and d5 next should black block.}) (10... O-O 11. Bc2 d6 12. Qd3 g6 13. Bg5 {With a crushing position.})