Sounds to me like you're struggling with what to build in your cities, and dealing with that by just building what the computer recommends. Sorry if that's not right, and also if what folllows is too simple. But playing as you seem to be leads to nothing except frustration because you're not in control and your civ isn't going anywhere.
Basically (and I'm glossing over other stuff here like great people and, if you've got BTS, espionage), all cities have four outputs:
Hammers
which you use to build units, or, well, buildings - the more hammers a city has, the quicker it gets the job done
Gold
which goes towards paying for the upkeep of your empire and can also be used for trading with other civs, upgrading units and so on. A city that generates more gold covers its costs more easily and contributes more to your treasury (top left of the main screen)
Culture
which expands your city's and your civ's borders - the more culture a city generates, the quicker its borders will expand, and the more likely it is to resist cultural pressure from neighbouring civs
Research
how much the city contributes to researching new technologies.
Underlying all of these are three features of every city:
Food
all healthy citizens need 2 food per turn. Any surplus goes into city growth, and when there's enough surplus, the city grows by one population point and its citizens can work one more tile. So the more food a city accumulates, the faster it will grow.
Health
how healthy your citizens are. There's a limit to how big a city can be before it becomes unhealthy. Unhealthy citizens consume extra food and so slow down city growth.
Happiness
how happy your citizens are. Again there's a limit based on city size. But unhappy citizens are worse than unhealthy ones because they don't work at all.
If you've got all that... Most buildings affect either the outputs of a city or its underlying features. So for instance a market increases gold output (and happiness if you have access to fur, ivory, silk or whale resources), a library increases culture and research, a temple increases culture and happiness, a forge increases hammers (and happiness if you have gold, silver or gems), a granary increases food growth and an aqueduct increases health.
And that should help you decide what to build. The trick is to maximise each city's outputs while also managing its growth / health / happiness effectively. So a city which is nearing the maximum size it can be before it becomes unhealthy or unhappy could maybe do with buildings which increase health or happiness and allow it to carry on growing. OTOH there's no point in building an aqueduct in a city which is comfortably healthy, or a theatre in one which is happy.
Mximising output depends on the land around the city which its citizens are working. A city which is working a lot of production tiles like mines could use a forge which increases those hammers by 25%. One that's generating a lot of gold could similarly use a market. OTOH there's no point in building a forge or a market in cities which don't have a lot of hammers or gold: 25% of not much is even less.
So stuffing cities with whatever buildings are available isn't a good play, despite what the computer recommends. There are actually very few buildings which all cities need. Most players would agree that all need a granary, and maybe a courthouse (which reduces maintenance costs). Beyond that it depends on the particular features of each city and its surrounding area, as above. And above all, don't forget to build units. If there are no buildings that would directly benefit a city, then build military units, workers or settlers instead. Once you research certain techs, you can also 'build' wealth, research or culture directly (by converting your hammers into each of them). Those are often better choices than another building.
Overall, there are no easy or fixed answers. It's all about choices and tradeoffs, and about making those based on the situation you're in. But if you understand the basics for making those choices, you'll go a long way, and learn more complicated strategies more easily.
