Annual Work Review

How do you draw a distinction between people pleasing and doing what the boss wants you to do without question because if you try to discuss other options they become defensive?  I used to try and explain my different perspectives on things and I think it made my boss start targeting me as a “trouble maker” for her.  I have been trying to repair the relationship but feel like I am being a people pleaser now…but she certainly has started to treat me better.  Suggestions for how to remain in silence and not feel like I’m not having my back?