Was Birdemic intended to be a bad movie?

The very short answer is no. Nguyen seems to be genuinely insane unaware that his movie is laughable. He honestly believes that audiences are laughing with the movie and that it's an intelligent 'think piece' and a romance film (!) to boot.

If you want to stare into the eyes of madness, you can watch the interviews below

Interviewer: "Do you think it's a good film?"

Nguyen: "I think that it's a good film, based on the condition of what I had to work with"

and

I see a similar pattern, is that the audience really likes the film. I think the majority of the audience [are] really laughing with the movie, and they were really experiencing the scenes of the film, scene-to-scene. It’s like they were sitting at the midnight showing of the ‘Rocky Horror [Picture Show]’. You know? - _{^{http://bloody-disgusting.com/interviews/23593/special-interview-birdemic-shock-and-terror-director-james-nguyen/}}