It is hard to say why you are not accepted.
I think you are right that your GPA, combined with your publication record, is a big part of the reason. The other big part is that you are an international student.
Usually, schools are looking for students who have excelled in some way in the past, for example, having a high GPA or being productive research-wise. A 3.0 GPA isn't very good (grad students in the US are generally expected to have been better than B students in undergrad) but it's not so horrible that you would be automatically rejected either. Similarly, it's pretty common for most new grad students to not have publications. But I think the combination of these two things make it very difficult for a committee to admit you.
In addition, you are an international student (I am one too). At public schools, international students cost a lot more, sometimes by a factor of 3. Therefore, because there is limited funds, there is a practical limit on how many international students they can admit (usually there is not a strict quota) so in essence, you are competing with other international students for a smaller number of spots than an American grad student would. This basically means it is a lot harder to get admitted as an international student at a public school and this amplifies the issue from the previous paragraph.
Here are some things you could do to help improve your application for future years (if you don't get in the remaining schools):
1. Apply to private schools or schools that do not charge a higher rate for international students. Even though private schools are higher ranked and may appear more difficult to get in, for me, I got accepted into higher ranked private schools and rejected from lower ranked public schools.
2. Continue building your research experience. Hopefully you can get a publication out of your work soon? From your profile, you sound like you have a lot of experience now, but the fact that you don't have a publication is a little worrisome. Maybe you can set a goal to write some papers and discuss this with your supervisor to ensure that you are on projects that can lead to something fruitful.
3. Consult with your letter writers. They would know you the best and maybe they can offer more useful advice!
4. What are your General GRE scores? If they are low, then maybe improving these would help too.