Are you new to running? If so being sore would be expected (at least I was). If you want to keep running to meet a goal, start slow and easy. As a starting point, take a look at some of the beginner running programs for a 5K race. Many of them will have you begin conditioning with several weeks of jogging/walking then build up slowly. Also make sure you have good shoes. It does make a difference.
If you are running for cardio conditioning (as opposed to a 'running' goal) there are plenty of other options that won't have you poundng away. For machines try cycling, ellipticals, versa climber, or rowing. If you like swimming, hit the pool.