There's two main reasons.  One, there's a clash of values.  Elizabeth definitely has a more old-fashioned view of how relationships are supposed to work, and sees Eleanora as not acting like how a good wife is supposed to act - her outspokenness, her relative immodesty, how she has Jonathan in the palm of her hand.

Two, she can see how Eleanora is really out for herself.  That's the biggie.  She doesn't think Eleanora loves her son, and would break his heart and betray them all if she thought that was best for her.