You can't help the writer if you aren't being honest with them. Don't feel like you can't be critical--that's kind of the point! If something isn't working for you, say so. If you are bored during a chapter, say so. If you find the main character unlikable, say so.
Don't take the "I must be critical" advice in the wrong direction. You don't need to be all "Doctor House" here. Beta reading is not an opportunity for you to get your snarkfest on--not unless you specifically know that the writer will find this funny or helpful. If you derive some sense of satisfaction from ripping someone a new one, tap that crap down when critiquing. Be professional. Be kind. Be mindful that you are trying to be helpful--and being unnecessarily hurtful is not usually helpful.
When you're being (helpfully and kindly) critical, don't simply say "I didn't like this chapter." Vague feedback is unhelpful feedback. You could have disliked any number of things, and the writer will have a hard time fixing something when she doesn't know where to start. Instead, say "I found the pace too sluggish" or "The dialogue in this chapter was unrealistic to me" or "When the main character complains all the time, I lose sympathy for her," etc. And then expand from there--give specific examples, and perhaps suggest some changes.
Offer both positive and negative feedback
Remember, your ultimate goal should be to help the writer. If you only succeed in discouraging the writer, you probably haven't helped them. Some crit partners fall into a "negativity rut" and only talk about what is wrong with the book or short story they are evaluating.
I like to say two positive things for every negative thing when I'm critiquing--it makes the negative things more palatable, and it helps keep the writer from becoming too discouraged in the fact of all the problems I may have found.
Don't try to make the book into something it's not
Remember that this isn't your book. Your goal is helping the writer, and that means encouraging and shaping their artistic vision for their project. If the book is a young adult paranormal thriller, don't suggest that the writer turn it into a contemplative, contemporary literary novel. Don't insist on making the book something you'd write. Your goal is to help the book be the best it can be as it is, not as you might make it if you were the writer.