Blossom End Rot, or BER:
According to the most knowledgable expert on tomatoes that I know of (Carolyn J. Male*), BER is caused by early season stress. "This includes too much fertilizer (causing too rapid plant growth), uneven delivery of moisture, and high winds (Which cause drying). Any or all of these stresses cause calcium to leave the fruit and go into the main part of the plant, and this lack of calcium in the fruit allows the black spot to develop." [ Because small cracks can develop at the blossom end, allowing the introduction of bacteria into the fruit.]
What to do? First, test your soil to determine whether sufficient calcium (Lime) is present and whether the PH is proper. Avoid over fertilization ealy in the season. Mulching may help keep moisture constant, but heavy rains may always interfere. In addition, some varieties are resistant to the malady, so always grow several varieties.
Carolyn is a professor of microbiology at the College of Saint Rose in Albany, New York. She has raised more than a thousand varieties of tomatoes in her garden.