I am assuming I was in a similar place like you 8-10 years back. In retrospect, I have found that the following reasons affected my applications.
1. I was from an unknown college in an unknown place. Yahoo! or Microsoft wouldn't even look at my resume. Too much of unknown.
2. Startups wouldn't hire me as relocation is expensive and 8-10 years back the good startups were scrappy. Btw, aren't the best ones always scrappy? And you might have been applying to them as you want to work with the best.
3. I listed a lot of expertise which I had. But its hard to believe especially for HRs who get 100s of candidate everyday advertising they know everything only to be told by the interviewer that the candidate wasn't good. I am not doubting your skills but the problem is the noise. Most 23 year olds don't know how to read code.
How I overcame it and got a job.
1. I did my Masters so an MNC would hire me. I knew this hack/entry.
2. After getting into the MNC, I worked my ass off and kept applying to jobs focusing on the work I did at the MNC.
3. I got a job at an awesome startup!
And things started changing. Now I get replies to most of my applications.
And automated or copy paste resumes do work but HN crowd might not agree. But most of the industry is still very non HN.
Hope it helps. All the best and keep applying!