It's true - although women have two X chromosomes, only one out of these two is active. The other one degenerates and forms a tightly coiled form of chromatin called a Barr body.
However, the crucial thing to note is that which one of the chromosomes is inactivated in any particular cell is essentially random. The 'choice' as to which X chromosome to ditch is made at around the 12th day of life (in the uterus) and is random; from then on, all the descendants of these cells will inactivate the same X chromosome. Nonetheless, this is still enough to ensure that around 50% of the cells in your adult body (if you're a woman!) use only the X chromosome that came from your father, whilst the other half use the one that came from your mother.
And this explains why X-linked disorders are far less common in women than they are in men. Let's say that a woman inherits a bad version of a gene on the X chromosome from her father. In around half her body's cells, this chromosome will be inactivated, and so the normal X chromosome (from her mother) will have full expression. This is usually enough to avoid showing symptoms of any deficiency. Men have no such luxury, of course - if one X chromosome is bad, they have no backup one for other cells to use.