A 3.0 GPA is the absolute minimum GPA a school will consider for graduate study. I was in the same position as you when applying to grad school (published paper, three research internships, top school, 3.7 GPA however) and the only physics grad schools I was admitted to were ranked over 100. I didn't apply to every school, but apparently reached far higher than I should have, despite advice from professors. But that's OK. I later found out that grad school rankings in physics is directly related to the number of PhDs they graduate each year. Smaller programs aren't bad, they're just smaller, and might be a top school in a particular subfield. I still got a top postdoc and my dream job from a lower ranked grad school.