It's a double standard because we know that whatever Lois is working on, it's got major ramifications. She's not just hanging out in a motel sipping drinks and relaxing while her family toils at home. This isn't just another book or article she's working on, it's big. Whatever she's learned, she's acting on it and doing her best to protect her family, and quite possibly the world. She's not punching bad people in the face but what she's doing is still a heroic act and a sacrifice. Clark leaves his family all the time for similar reasons, often doesn't tell Lois all the details (or outright lies to her, which he does a lot) and everyone is cool with it. But Lois doing the same thing is getting all kinds of hate, and we don't even know what her reasons are yet. Fans just see Lois doing her own thing, and immediately assume the worst.
She and Clark still love each other, they're still married, they're still happy. The only thing going on right now is that Lois' job is keeping her away from home for a little bit. And she knows that her husband and son can get by without her around for a time. It's not the big deal a lot of people are making it out to be.