To go to the amazon you can fly from Bogota to Leticia, from here you can arrange many tours into the amazon, though it is cheaper if you were to go from Peru or Bolivia.
The coffee region of Salento is a good place to experience the coffee farms from both a large scale and small local farms. The people in the region are really friendly. From here you can visit the tallest palm trees in the world , which stand at around 50 feet tall. The circuit walk around the palm tree forest and taking into account a little break at an elderly couples farm to see hummingbirds and buy a drink, takes about 3-5 hours.
If you don't have time to visit the lost city but would still like to see how some of the indigeneous people live in the traditional villages you should head to Minca, there is a german couple living in there who have befriended a local tribe and can bring you to visit the village. They can arrange 1 / 2 / 3 night hikes to visit them and the surrounding mountains. If you are interested I can let you know how to contact them but you should also know that if they think you will be disrespectul or take a disliking to you they won't show you the way......... Thats one of the reasons I liked them...............it was nice to think that when we were there , they had previously only brought two people there......
Otherwise there is also a chance to check out the caribean with Playa Blanca and Cartagena.
I hope you have a great time in Colombia, its one of my favourite countries ever !!
while in Bogota pay a visit to the gold museum.
poorbuthappy.com has all the info you are looking for-or most of it anyway.
I found bus travel to be very safe, nice busses too!
The northern coast is great, Santa marta is a bit of a dump, but great national parks and beaches around there. I don't recommend swimming at the beach in the city..yuk, but the water in the tayrona nat park is crystal clear and warm, and the walk through the park is pretty cool too, lizards, monkeys, ants.
If you have time for the lost city trek, do that for sure. Was one of the best experiences of my trip!