France's navy was more or less a fleet under siege after 1805, very much restricted to its own ports, the bulk of its Squadrons rotting away on the West coast (Channel Coast) of France. The cause for this was a non-stop British blockade to prevent, at first, a perceived threat of a descent upon the British Islands, and later, to attempt to precipitate the economic ruin of the First French Empire. The rest of the British fleet was hard at work making sure France could not gain another fleet like it did in the 1790s and early 1800s with coup d'mains in Holland and Spain, and this brought the already hard-at-work Royal Navy to its absolute breaking point, bringing it into notable naval conflicts with Denmark and the United States of America due to their attempts to seize and search neutral shipping.

Source: David Chandler; The Campaigns of Napoleon, 1973

Spain's navy was shattered at Trafalgar, and by 1805 Spain's Bourbon dynasty was very much under Napoleon's magnetic personality. Spain would later be involved in a titanic struggle during the Peninsular Wars of 1809, 12 and 15; of which Britain would also be a major player. The Catholic Church was occupied by the First French Empire and its military might, nominal at best to begin with, gone. The Knights of St. John were wrested from Malta, never to truly return as a military power, in 1798, and the Greek Islands were the playground of diplomats for the duration of the Napoleonic Wars, with Islands such as Corfu - coveted by many, needing large garrisons that could not be spared for anti-piracy operations.

The conclusion therefore is: Everyone was quite pre-occupied in one of the largest struggles to date. The British Royal Navy was stretched to its absolute breaking point in securing communications to India, the Americas, protecting the homeland and keeping the remnants of the French and Spanish fleets in their home ports.

Edit: I talked with some other flairs, and more information was handed to me that should satisfy you; quite a few European states were paying bribes that protected their shipping from Barbary pirates, and was considered an acceptable cost for keeping them away from their own ships. Militarily, it meant that one did not need to dispatch a squadron and further dilute the concentration of naval power, and politically, it meant the Pirates would have to attack another State - perhaps even one of their enemies. The British had the money and time to pay the Bribe, the US did not, /u/Georgy_K_Zhukov cites that the US had to pay, by 1800, almost 20 percent of its annual budget if it wanted to meet the requirements of the bribe, and thus decided military action was more cost effective.