Agencies act on behalf of the employer, not the jobseeker. It is in their interest to fill each post with a willing applicant, so in most respects the interests of both sides should be met. But if any point of conflict between the employer and the prospective recruit should arise, agencies will tend to side with the employer because that’s who is paying their fee.
It’s also worth remembering that recruitment agencies are not careers advice centres, and are usually not qualified to help you with career decisions. Their role is to find people to fill positions for their clients, so don’t be tempted into thinking that an agency’s main concern is your career satisfaction. Some agencies will have no hesitation in trying to talk you into a job that you feel is unsuitable. If they do, don’t feel under any obligation to take it. You’ve gone to them to help you find the right job, not the wrong one, and if they get stroppy then go elsewhere. There are plenty of other agencies to choose from.
The same applies to your CV. Write the CV that you want to show the world, and only make changes suggested by the agency if you’re completely happy with them. It’s your CV and your career.