No, Muslims in Switzerland should not be fined for wearing burkas. People in Switzerland are supposed to enjoy certain freedoms, including the freedom of religion. People who are Muslim should not face fines or penalties simply for following the tenets of their belief systems, and it is unfortunate that Switzerland has taken that approach.
We hear often of the phrase "separation of church and state." If the Islam religion dictates that women shall wear burkas, hijabs, or niqabs, they should be allowed to do so without Swiss government attempting to fine them. There are no laws in Swiss government that say that all women must not wear any head covering of any kind. So why does this only apply to Muslim women? It is unacceptable.
There is absolutely no excuse on imposing penalties on people's religious customs. Tolerance is one of the key values that Europe is striving for, and fining Swiss Muslims for wearing burkas is an inexcusable example of discrimination. It is sad and surprising that in 2013 the law prohibiting burkas was backed by 65% of the vote in the region. This conflict of belief highlight the need for more dialogue between people of different religious allegiances.
Firing someone for wearing clothing specific to their religion, unless it is grossly offensive (e.g. swastikas, hate speech, etc) is ludicrous in the extreme and demonstrates an appalling level of racism. Firing someone based solely on the fact that they wear burkas constitutes religious discrimination and should be punished accordingly. Burkas are harmful to no one expect those who make a special effort to take offense.