Chiming in with what seems to be the majority opinion that you can be direct with your friend and not be breaking any etiquette rules. It might be a difficult conversation, and I definitely sympathize, but it's not wrong to be honest.
"Friend, I have to be direct with you and say that since getting a Nexus card, and being able to get across the border faster, I really don't have the patience to sit in the regular line. Plus, frankly, it's hard to justify spending the time that way instead of spending it where we want to go. I really like doing stuff with you, but at this point I have to ask you to get your own Nexus card if you want to keep doing these trips on a regular basis".
It's a given that we're not supposed to assume things about other people's financial circumstances, but if these are shopping trips, and if your friend is giving you money for gas, a $50 fee for five years is probably not an impediment. As others have said, it is possible that your friend did apply for a card and was turned down. But I wouldn't put her on the spot by asking if that's the case. She can choose to tell you if that's the case, at which point it's a different situation ("can't get one" vs "won't get one").
(BTW, I used to live in Vancouver and am familiar with several border crossings between BC and Washington, and have also done the "wait forever" thing. I live in Toronto now, and crossing around the Niagara region can be just as bad. If I travelled to the US often enough, I'd be applying for a Nexus card of my own.)