Edit: Currently doesn't work. Game crashes after a short period of time. Use DxWrapper w/ Stub/ddraw.dll for now instead with the following settings in dxwrapper.ini:

Dd7to9 = 1
DdrawFixByteAlignment = 1
DdrawOverrideWidth = 640
DdrawOverrideHeight = 480
DdrawIntegerScalingClamp = 1
DdrawMaintainAspectRatio = 1

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Get cnc-ddraw zip from here[github.com]
Extract the contents of the zip directly into the Tropico directory
Run "cnc-ddraw config.exe"

Here are the settings I use:
"Borderless" or "Fullscreen Upscaling" works well
Check "Maintain Aspect Ratio" if you don't want the screen stretched


I use DirectDraw to "OpenGL" for the shader support - selecting nearest neighbor is sharp, but you might want to use a different shader if you like smoother outputs.
Direct3D 9 can also be used for best performance
GDI for best compatibility
All should work

I also enabled "Integer Scaling" for pixel-perfect output, though you can disable this to fill the height of the screen.

Run "Tropico.exe" or from steam and it should execute with the wrapper.