Good question. Indeed 4..bxc6 is extremely rare compared to the main line, and the reasons are multi-fold specially strategically, but foremost, from a concrete point of view it leads to a rather poor position for black after the immediate d4-exd4-Qxd4 and white's completely controlling the centre:
[title "Important concrete reply"]
[fen "r1bqkbnr/2pp1ppp/p1p5/4p3/4P3/5N2/PPPP1PPP/RNBQK2R w KQkq - 0 5"]
1.d4 exd4 2.Qxd4
From a strategic point of view, 4..bxc6:
leaves black with an isolated a6 pawn without any effort required from white.
More damaging to the structure than dxc6 as black's left without any prospect of a queenside expansion since move four already! First repercussion of the latter is the fact that white has the assured prospect of blockading black's isolated a pawn and in doing so render it into a permanent weakness.
Despite black having the bishop pair in principle, the bishops have very poor prospects in this structure, in particular the light squared one, e.g.: developing it along the long diagonal is no longer meaningful as the fianchetto option is gone and an indirect one with c6-c5-Bb7 will in turn block-in the f8 bishop. Moreover, to develop the bishop along the side diagonal c8-h3 is now at least delayed for an extra tempo, which means white could easily include h3 without any real drawbacks. Instead, with dxc6 both bishops are immediately activated and the bishop pair compensation is more tangible (specially with Bg4 being readily playable).
The latter is really pointing to the fact that with bxc6 black is left with very poor piece activity, and the structure guarantees no real outpost for the knight, in fact not even the immediate Nf6 is playable after bxc6 d4 exd4 Qxd4 Nf6 the knight is pushed around to non-ideal posts such as b6 or e7 after e5-Nd5-c4.
Unlike bxc6, dxc6 is in fact challenging the immediate d4 (which is one of white's main plans in this structure) as the queen trade becomes forced and having the bishop pair black definitely doesn't mind the endgame. Thus, as mentioned in the beginning, with 4...bxc6 black is even playing into white's hands by inviting d4.
This line of bxc6-d4-exd4-Qxd4 is really critical as it perfectly highlights the major differences between the two sides: white has all the space, perfectly healthy pawn structure, ready to castle (while black is at least 2 tempi away), while black has no prospect to claim the centre, nor to liquidate the isolated a6 pawn. I highly encourage you to play through some of the ensuing lines after this move order, you'll quickly develop a feel for the kinds of struggles black is facing.
Now consider going through all above points but with the position after 4...dxc6:
[title "Main line after dxc6"]
[fen "r1bqkbnr/1pp2ppp/p1p5/4p3/4P3/5N2/PPPP1PPP/RNBQK2R w KQkq - 0 5"]
in doing so, hopefully you'll be able to convince yourself that all the aspects of dxc6 outweigh that of bxc6, both concretely and strategically. Last but not least, note that here the immediate c3 (for d4) is not possible due to Qd3, moreover, black is well in time to keep the fight over d4 alive (e.g. 5.O-O Bg4 pinning white's most important piece of they're to ever play d4).
At the high level, the key downsides to be emphasized for 4...bxc6 are: isolated a pawn, no prospect of expansion on the queenside, extremely limited minor piece activity, delayed development, and the lack of any ability to create a target in white's camp.
4... bxc6.