When employees resort to writing to their boss's boss, it is often the last resort. Typically this occurs after they have repeatedly gone to their boss to have a situation resolved, only to be dissatisfied with the ensuing action or inaction.
It is normal for you to be upset and even embarrassed. However, rather than acting defensively or vengefully, you and your company will be better served if you step back, think about what the employees wrote, and then get together with them to jointly discuss their concerns and establish some specific steps to resolve them.
This does not mean that everything in the letter was correct. In fact, the letter could be totally wrong. After all, it is based solely on the employees' perceptions of you as a leader. But, if their perceptions of you are negative, that is reality for them.
All of this means that the best step is for you to get together with your employees to figure out a more productive way to work together. Although it may be tempting to tell them the countless ways that they are wrong, such an approach would be wrong. These employees want to be heard, and your best approach is to be all ears.
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