If you are Germany, and intend to have a naval force operating in the WMed or SAtlantic, then you can forestall Allied use of fighters against this fleet by stationing inf in Gibraltar.
Perhaps also by taking Gibraltar early on, you give Allies the impression you will be striking out into S Atlantic. Thus they may devote some energy & material in that direction; could be a reasonably good low-price diversion.
Of course, after 99 years you will have a messy political referendum on your hand as Spain presses for “reunification” of its former possession. Ach du lieber!