You look at the line of red rings on your radar (when the returns inside the thunderstorm get up to 'Oh my God!' level, they are cancelled so storms show as rings- easier to see through the clutter), try and pick a route through if you can, or deviate as far as it takes, then strap 'em in and go for it Baby! You are going to get shaken around. This is what you have to accept if you are going to fly aeroplanes through tropical regions (if you want to get to your destination).
It is standard practice for certain nervous passengers (and if I may say, many Americans) to get off the aeroplane (often on their knees) muttering words like 'lawyer', 'sue', 'shotgun' etc. One can only say it is 'safe' in that any form of transport is 'safe'. There are very few incidents of aeroplanes entering a thunderstorm and not coming out of it in the same number of pieces- it is exceedingly rare for tragedies to occur. Nobody likes being shaken about, but for some reason, many people think that despite the fact they want to travel by air, there should no risk whatsoever borne by they themselves, and any rattling around is automatically the fault of the airline or crews!
It comes with travelling the skies!