There was a more traditional flag (red-white-blue) in the ZIP but the reference to it was not correct. Now, if you would like to use this flag instead of the black lion on orange you should edit the CIV4ArtDefines_Civilization.xml file.
ORIGINAL:
<CivilizationArtInfo>
<Type>ART_DEF_CIVILIZATION_NETHERLANDS</Type>
<Button>,Art/Interface/Buttons/Civilizations/Netherlands.dds</Button>
<Path>Art/Interface/TeamColor/Dutch_Flag_005.dds</Path>
<bWhiteFlag>0</bWhiteFlag>
</CivilizationArtInfo>
NEW:
<CivilizationArtInfo>
<Type>ART_DEF_CIVILIZATION_NETHERLANDS</Type>
<Button>,Art/Interface/Buttons/Civilizations/Netherlands.dds</Button>
<Path>Art/Interface/TeamColor/Netherlands.dds</Path>
<bWhiteFlag>1</bWhiteFlag>
</CivilizationArtInfo>
Important: The "<bWhiteFlag>1</bWhiteFlag>" is so that
not all white will be made transparent.
I personally like this one better and with keeping the orange borders it all looks very Nederlands
