Because Sam's greeting is usually held as indisputable proof of Sam's 'heterosexuality,' while his similar interactions with Steve that immediately proceeded Nat's arrival, are virtually ignored by the majority of fandom.
The biggest problem with the way Natasha is handled in Winter Soldier vs. AOU is that her entire being in AOU feels compromised due to the elimination of Clint/Natasha and the entire context surrounding her relationship with Bruce.
A weary Natasha who grows closer with Bruce, initially as friends, over commiserating about their life choices? I have no problem with. Natasha as a windswept rom-com heroine paired with bumbling, yet intermittently dashing nerd Bruce, is textbook Joss. They're virtually a replay of Wes & Fred, replete with the requisite sad clown hero wallowing in his man-pain and the reduction of a multi-faceted female character to a generic love interest imo.
Plus their whole connection, such as it was, was rushed. They had a small yet interesting arc in the Avengers, that is essentially dropped, then suddenly they're acting like Bogey and Bacall in AOU.
It also didn't help that Natasha, by virtue of being the only female Avenger, at the point had the burden of being the only representation in terms of gender, and had already had significantly established relationships with both Tony and Steve. Unlike every other male Avenger, including Bruce, who had various love interests outside of the team.
If Marvel hadn't dropped the ball and committed to a Black Widow film in Phase 1 or 2, many of these issues could've been resolved. But now, in the wake of Wonder Woman's success, they're scrambling to rectify their mistakes, but much like the issues with Steve/Sharon, the damage is already done.