If Natasha hooked up with some random shield agent, and then dated Bucky, it wouldn't be much of an issue... but we're emotionally invested in both Hawkeye and Bucky, so it creates more uncomfortability
That said, double standards are kind of all over the place, both in comics, but also even worse in Hollywood.
It seems comics take a lot of heat lately for something they do better than many other mediums
Here's the thing, though. She doesn't do hook up. She was in a monogamous, committed relationship with each of her love interests. It isn't as if a typical Black Widow appearance has her showing up in some random dude's bed.