I hope you get better advice as the days progress.
I do not use After Effects for encoding. I render out of After Effects to a stable video format like Animation or DV. Then I take that movie into an encoder application such as Apple Compressor, Adobe Media Encoder, or Sorensen Squeeze.
H.264 can increase your file size if you do not set the parameters properly.
What are the exact settings you use? Depending on the resolution, you may never be able to get below a certain data rate. also keep in mind, that also the profile levels do matter, since they dictate the smallest and largest possible block sizes and matrices and thus also hugely influence compression efficiencey. Last not least, have a look at your audio compression. It may considerably contribute to the overall file size...
To give us a better idea, what is the length of your video, the resolution, the size you'd like it to be and the size your are actually getting ?