Impact resistant glass is one way to handle it, but in areas where the design wind speed is in excess of 130mph, we have found it necessary to specify shutters that may be attached, rolled down, closed or whatever to protect against debris damage.
One thing to keep in mind as well, every fenestration product (among other things) MUST be tested by a Florida approved testing agency, then the results must be submitted to the state for "Product Approval". If the state agency approves the application, the product is assigned a "Product Approval Number" Without these product approval numbers you will not be able to obtain a building permit. You will also not be allowed to use any product that is not approved, even if you have permits. From the agencies I have dealt with, the cost of getting approval for a single product can be as low as $25k and as high as $80k depending upon the number of tests required. It certainly is not for the faint of heart, thats for sure.
If you want to find doors and skylights that are approved, you should check out
this page A word of advice is to leave all fields as "Select All" except the product type you are looking for.