How come my Adobe Illustrator file doesn't show up in After Effects?
Are you manually animating in illustrator and then bringing them in as individual frames in After Effects or are they independent assets?  After Effects treats Illustrator files as images that are displayed across multiple frames and the background is transparent.  You then animate them in After Effects itself by positioning and scaling and such.

If you have multiple layers in Illustrator, you also need to decide which layers are imported as your asset.  You can either flatten it or use individual layers when importing.