Do universities care much about the transcript if you apply for an?
Yes it matters. Performance at school is generally a strong indicator of performance out of it. So employers normally screen for it. However, it is not the only thing they look at. Unfortunately, it is one of the first things they look at and screen from. So it is possible a non-technical recruiter screened your resume out simply because of your GPA. I suggest you can the employer to inquire about your application. If they moved your resume to the "active file" then you are no longer in the running.