I have this problem as well. Most times, I don't want the Droid in the dock mode when I have it in my car dock. It messes up my Home++ and causes a lot of Force Close errors.
I also use the Verizon hard rubber snap on case as well as a large horizontal leather case to carry my Droid. I solved the problem with the Droid waking up from the case's magnet by turning the Droid so that the screen side is facing out toward the magnetic closure. The Droid only wakes up when the back of the phone is facing the magnetic clasp on the case. I would preferably want to keep my Droid in the case with the glass screen facing toward my body for protection, so I might check out that Dock Blocker app. Thanks.
Edit: Just purchased the Dock Blocker app. It seems to be working for my leather case with two magnets. The screen comes on for a second or two, then will return to standby. Good stuff.
I will try it out in the card dock later.