Recreational running is probably not harmful to your hips and may actually be beneficial. Some research has suggested that runners have a lower incidence of hip osteoarthritis than sedentary individuals and competitive runners.
Your muscles and bones adapt to the forces placed upon them so are likely to become stronger with running. Exercise often produces pain reducing effects so may help your hips feel more comfortable.
However, if you have suffered a previous hip injury or are currently suffering with hip pain please do seek professional advice before starting a new exercise program.