The fundamental thing to understand is that the Federal Council, as the collective government and the head of state of Switzerland, is collegial and bears collective responsibility similar to the situation in the Westminster system (even if nowadays you may assume it is a given due to the strong party discipline practiced in several Westminster countries).
And if every (major) party is government, every party is also opposition. Collegial and consensus-based decision making also means no party will get all it wants on every issue; compromises are made on different issues along different lines. The compromises and the consultations do not guarantee that the same line would be followed by the Parliament at large. A project may be seen as too extreme or not radical enough at the same time by all sides of an issue.
The Federal Council, once elected, is semi-independent, but subsidiary. There is no impeachment process within the ordinary political framework (an adhoc constitutional amendment, of course, can be initiated by the parliament or the people). Unlike in Westminster systems, the executive does not directly face a question of confidence at all times. The separation of powers gives space to criticism, divergences and debates.
The Parliament remains supreme and can adopt motions to direct the Federal Council's priorities and to ultimately decide (subject to referendum) on proposals of the Federal Council. Like in the Westminster system, motions are binding upon the government unless it interferes with the government's constitutional prerogatives. In Switzerland, the Parliament can direct the Federal Council to initiate a bill or take certain measures via motions. The Parliament can demand the Federal Council to draft new laws or modify proposals, e.g. on agricultural policy and participation in eu-LISA.
The parties alone cannot force "their" councilor to do anything if others do not agree. They rarely criticize individual councilors for their political positions, but instead treat the Federal Council as a collective. They are not harmed by criticizing the Federal Council's position as promoting their own policies in and out of Parliament is more important. The parties happily launch referendums against laws initiated by the Federal Council and passed by the Parliament.
But individual Federal Councillors are criticized, of course, for the handling of their individual portfolio. A Councillor is seen as the Minister of Interior or Justice or Economy, not the Socialist or Liberal-Radical or SVP/UDC Minister. Even then, direct attack on individuals for policy decisions is often seen badly across the political spectrum (but does happen).
Additionally, party disciplines in general are weak in Switzerland. Each cantonal and municipal section, as well as the youth sections (and other subdivisions) often have contrary positions on many issues and may issue different recommendations in referendums (e.g. on same-sex marriage and access to IVF for lesbian couples). Regional and linguistic diversities and differences do exist within political parties.