Did you read any game tips? (they are scattered through walkthroughts and forum topics)
First you have to low navigation for your new shiney frigate (you get stat penalty and officers/crew salaries are crazyly high etc) so do one of the following:
- leave it to port controller and just focus on "land" missions for a while + forgotten logbook (ship controler) quest for nice navigation skill boost
- hire minimum crew, sell all canons and just have minimum of food, medicine and room onboard and do merchant missions (much higher income, your frigate should have nice max cargo which influence quest reward) while ignoring your crew pleas for money (quest officers always have maximum loyality and you can just ged rid and hire new crew or even sail without any crew i think (player controled ship only, rest won't be able to enter world map mode without minimum crew)), also you can save/load into some pirate capitans quest (for low lvl i doubt you can finish anything different than the one when you fight some shipwrecked people for gold/silver etc) that also give some nice amount of gold
In both cases you have to unfortunetly forget about good old pillaging :< Just focus on becaming stronger and getting some nice items and improving your navigation skill (quest mentioned earlier and sailing in storms or attacking a fort (with frigate from quest and just run away when things get ugly (not sure if repair cost is affacted by to low navigation skill but it will cost quite a lot for low lvl character but both skill and exp/lvl gains are simply crazy... before you notice you have 100 navigation/artilery/accuracy and like ~40lvl

))).
When you lvlup you can start pillaging or do same harder quests... i did COAS quest at like lvl 10 or so which was really hard at times (few really hard fights for that low lvl) and when i finished it at like lvl 14 i think with few of the best items in game from quest rewards game suddenly became horribly easy and i even captured two man-o-wars in one battle (though i had to load save before this sine i had bassicly no crew left and five hostile ships on my tail with badly damaged sails).
Also do some of the easier quest - Austin and maybe killing the beggars (just don't hurry into COAS since it take a lot of time and is rather hard though fully cleared give many great items and like 2kk+ gold and great third class ship) and just hang out there. Sadly there is big jump in game difficulty and after very grindy and long start quickly everything becames so easy it's boring since you can even pillage smaller cities with just one class 3 Corvet
Also few more tips:
- upgrade your ship cargo capacity in pirate settlement shipyard when you can afford it, you'll get more gold from merchant quests (sine you can ship more cargo) and it's generally usefull, same with max cannon caliber unless you have 32 or more already (culverines 32lbs are best cannons you can get unless you get your hands on class one ship. 48lbs cannons are a little more powerfull and have better range but reload slower) and if you cannot get 32lbs even with upgrade... just change your ships since it's crappy.
- don't let your quest officers die and preferably get experience exchange skill rather early
- to get into enemy cities even with flag change you need A LOT of stealth (even with 100 i get discovered sometimes and it's probably one of the worst aspects of the game... dunno even how they recognize you when you are only hostile and don't have bounty on your head) so just get to it by land during night and get to tavern (often it takes a lot of work and save/load if it's governor mission) and do what you want during day but still stay away from guards
- well... grind
For more just brows the forum a little i'm not a specialist since i got bored when there was no more challenge after COAS and when i finished almost all the non repetive quests.