Why do recruiters say that someone is not qualified for a position, when they are clearly qualified for the job and in most cases "over qualified" for the job (according to their resume)?

Recruiters are specifically told by the company they are seeking candidates for exactly what that company is looking for and it can vary from company to company. Although you personally may feel you meet the qualifications, in this market, there are an overwhelming number of applicants that probably meet exactly what they are looking for. If they see that you may be 'overqualified', there is a risk in hiring you because you are more likely to jump ship when you get a better offer somewhere else.
I would suggest you tailor your resume for each position you apply for and include a cover letter. Another great way to get jobs is through networking and joining professional associations- most jobs I've gotten have had nothing to do with submitting my resume to a recruiter and more through meeting people in that field.