What do the red and green circles in my vehicles list mean? Profitability?
Pretty sure it's profitability.
Is there a manual for this app?
If you're genuinely playing TTD, which due to the high difficulty in running it on modern computers I doubt, then no.
Some of the bus stops seems to have a very high number of passengers (like more than 100 or even 200), should I just place a ton of buses between them or is there a better solution?
Lots of buses would work. You could also consider trains.
People who downloaded this app also seems to often download an app named OpenTTD, is that just the lite version or is that a good game too?
I think it's fair to say that there are far more people who download OpenTTD than ever download TTD (or TTD Patch these days). OpenTTD is an open-source remake of TTD, with a huge array of new features/improvements/bug fixes. It can also run mods, known as GRFs, as well as custom AIs, and Game Scripts which give you a goal to achieve.