So, in order to ease your worries, we will clarify per destination:
The flights from Bogota to Guaviare that our operator uses are commercial flights much bigger than the plane that crashed. The airlines are SATENA and EASYFLY and the planes are normally modern twin engine ATR planes of 42 or 72 passengers (ATR42 or ATR72 planes). https://www.atr-aircraft.com
For traveling to San José del Guaviare from Bogota, we have to say that there is no problem and there is no difference in the risks than traveling to any other major city in Colombia.
But flight cautions have to be taken into account for some special expeditions to isolated places like Araracuara or Vaupés, where the flights can be different:
In order to get to Araracuara, our operator normally hires flights that use the Antonov 26 or Antonov 32 planes and the company for that is Aercaribe: https://aercaribe.com/antonov32/
Vaupés is a department (state) of Colombia and has a big airport in its capital, Mitú, that receives ATR planes from SATENA airline. However, once in Mitu, visitors can take other planes like CESSNAS in order to get to places less than 30 minutes away like Raudal del Jirijirimo. At this destination, there are not many options of planes, but our operator always checks very carefully the documents and of the security requirements of the planes.
Guaviare has definitely no issues and for the special expeditions to Araracuara or Vaupés, our operator will take extra measures and inform us in advance of the special logistics. However, that is why expeditions to Araracuara or Vaupés are very limited and have very few visitors.
What about other Amazon gateways?