What are the main differences between SAP2000 and Etabs ?

As the name states ETABS( Extended Tridimensional Analyses of Building Structures), this program is mostly used for design of   highrise building structure. While SAP2000( Structural Analyses Programme) is a general purpose analyses software which can be used for any building or non building structures.

The answer to your primary question is that both are used for various aspects of building design depending on which tool is best suited for the application. If there is a more specific question regarding a particular application, I'd be happy to address that as well.  I will try to describe how we utilize both of these tools in current practice. Perhaps this will help bring the strengths of each to light.  SAP2000:

• This program is primarily used for gravity analysis and design
• This tool is often utilized for smaller structures, or portions of a larger structure. 
• It is great at handling complex geometry as it offers users a lot of different element types and a lot of customization with regards to meshing options.
• It can also be used for wind analysis and for more simplified seismic design procedures. However, it will take more data post-processing to retrieve the desired results for story drift, story shear, base shear etc.
• It lacks some of the simplicity that ETABS has of discretizing the structure into macroscopic elements.

ETABS:

• This program is most utilized for handling large scale seismic (or wind) projects, including those that involve Non-Linear modeling.
• It allows for more simplified modeling of the entire structure, enabling the designer to focus on macroscopic performance targets
• It is well equipped to handle simplified lateral procedures, Push-over analysis, Response Spectrum Analysis, and Response History Analysis.
• The data output options are much more conducive to lateral design

Please note that there are likely are some finer points regarding the differences between each program in regards to the analysis engine and solver. This is something only some folks from Computers & Structures Inc (the manufacturer) can answer.

SAP2000 is general program for structure analysis but Etabs specializes in structural analysis of the side forces