after effects file sizes

You have "transcoded"---you effectively converted your movie to being encoded by the Animation codec. The Animation codec is good at preserving image information; it's not good at making files small.

Your original movie was encoded using a codec that was good at keeping files small. After Effects unpacked this information to make a full image. You just didn't tell After Effects to stuff the image information back into a highly compressed form.

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Todd Kopriva, Adobe Systems Incorporated
putting the 'T' back in 'RTFM' : After Effects Help on the Web
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This is a huuuuuuuge question, and frequently asked.

Here is the very simple answer:

If you're encoding for final delivery, then you need to ask your client what they want.

If you're encoding for intermediate or archival purposes, then you should use a lossless codec. For 8-bpc work, I like QuickTime movies encoded with PNG or Animation, depending on the kind of imagery.

Here's a link to a section in After Effects Help about compression: "Encoding and compression options for movies"
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Todd Kopriva, Adobe Systems Incorporated
putting the 'T' back in 'RTFM' : After Effects Help on the Web
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