I think your question might get an answer here (Why can't we directly elect ministers), but there are some practical problems related to proportional distribution of government:
1. Small number of members - a government is composed of a relatively small number of members and it is harder to obtain proportionality
2. Not quite equals - there can be great differences between government roles, both at public perception and actual budget. Some will consider that leading country's Ministry of Defense is more important than leading Ministry of Culture
Also, the Government is the executive power and one should expect more "technicality" there (each member deals with a clear part of the State problems which, in theory, should require some knowledge/experience), as opposed to the Parliament which can be composed of "generalists", since they are approving most of the laws. So, a more "the man for the job" approach sounds more reasonable.
One possible example to illustrate this idea: it's reasonable to elect those who decide that a road should connect two cities, but not those who actually do the project management, coordinate the workers and decide materials to be used.