Only your doctor knows why she wants you to slow down, so it'd be a good idea to ask her. My OB told me that too...she actually told me no exercise for a few weeks, and to slow down at work as much as possible. She just wanted me to be cautious until I got out of the first trimester, when the chance of miscarriage is high. I always figure that when the baby's here my whole life is going to change, so I might as well get used to putting her interests first now.
If you're considered high risk then follow the doctors orders. Also, she probably doesn't want you to risk a miscarriage due to your busy schedule and strenuous activities. Proceed in moderation but you certainly don't have to stop, especially if running has been a part of your lifestyle. Travellin by plane is fairly safe thru 32 weeks, then car thereafter. Just make sure to move and stretch to avoid numbness and clotting. Good luck!