Even before she's Marked, Zoey isn't thrilled with her relationship with her mom, mostly because everything changed when she remarried. Zoey remembers that her mom "used to read exotic romances and actually wear makeup. Both were things her new husband didn't allow" (2.54). Looks like the new hubby runs the show around their house now.
So Zoey's not too optimistic about how her mom will handle Zoey being Marked, though she hopes "Maybe she would be understanding […] maybe she would know what to do" (2.50). But these hopes are dashed to pieces when Zoey's mom reacts with fear and anger: "Oh, God! What have you done now? […] What is your father going to say?" (2.60-62). Zoey's mom doesn't even try to comfort her daughter, who's been sentenced to becoming a vampyre, like it or not—she just worries about how things will look. Thanks for nothing, Mom.
This isn't the most mom-like thing to do, and Zoey calls her on it: "You haven't cared about anything but John since you married him" (2.74). Further, Zoey declares: "The truth is that because of him you haven't paid attention to your kids for three years" (2.77). This may seem harsh, but Zoey has observed her siblings when their mom isn't around, and even though they pretend to be perfect, they're getting away with all kinds of stuff behind their mom's back.
Further, Zoey's mom seems to care more about appearances than about her own kids' well being. During a discussion with the step-loser, Zoey's mom says: "But John, honey, what are we going to do about her? What will the neighbors say? […] What will people say at Meeting on Sunday?" (3.19). Um, yeah, because gossip is totally more important than looking out for your child's welfare.
In the end, Zoey decides to run away from home since her mom is clearly neither able nor interested in looking out for her. When Zoey lies about going to lie down, her mom "looked at me and nodded, telling me she was sorry the only way she could, with her eyes" (3.37). This is, sadly, a pretty damaged mother-daughter relationship, and it doesn't seem like it'll get any better until Zoey's mom reevaluates her priorities.