I found a workaround for this...
After much frustration & a lot of searching, I finally came across a very clever workaround for this issue in a Motorola Atrix-related forum. Cheers and many thanks to ACraigL (Andrew) for his original post.
Here's how to get around it:
1) Go to Android Marketplace and install an app called "Setting Profiles". The free Lite version will do the job.
2) Run Setting Profiles on your phone.
3) Create a new profile that turns off the speakerphone; call it "Speakerphone Off" or whatever. Hint: to create a profile that does this, clear all the checkboxes and all the green stars, then enable the green star for Speakerphone and make sure that checkbox is unchecked.
4) Create a new Rule with the following two conditions: Docking State=car dock and Active Call. Next, use Add Tweak to add a 5-second Activation Delay (this is required so the phone doesn't override the Speakerphone Off setting). Finally, choose Add Action, Activate Profile, Speakerphone Off.
Voila! All incoming and outgoing calls will now play through your car speakers via the Car Dock's audio out.
Note: If you have trouble on your phone, try tweaking the delay time. The 5 second delay works flawlessly on my Bionic; the original poster said he ended up using 3 seconds for his Atrix.
I hope this is helpful to other users.
best,
JohnB