Filters and transitions applied in FCP won't show up in Motion. That's just how it works - Motion looks at the underlying media. However, Any transformations from the Motion tab in FCP (scale, opacity, rotation, aspect, etc.) WILL come through in Motion, including keyframes. Thus Jim's good recommendation to keyframe opacity instead of using a transition. I do wish Motion would include some transition effects to accomodate this workflow issue.
Apple-certified instructor, FCP, DVDSP and Motion
Author, Motion Visual Quickstart Guide from Peachpit Press http://www.applemotion.net