Can You please ask low cost airlines of Europe, if any of these airlines is willing to fly to Zilina if the runway would be extended? Can You please contact such airlines? 

Can You please apply for funding to Zilina city authorities and regional authorities? If You did it already in the past, can You do it once more?

I come from Poland. In Poland, some airports were built only with local funds. The same might happen in Zilina. No central governement money is neccessary.

There is no airport on the Polish side of the border, nor there are big airports in proximity. You should use the chance. 

In my town a similar airport was revived due to subsidies for airlines to operate route Zielona Gora-Warszawa. In Your case, the line to Prague was closed. Such a route should have been subsidized, as this is "infant industry" and infrant industry argument says that such businesses should be financially supported for a while, before they will develop and mature. In Your case the offer of passenger flights to Zilina was a very short episode. 

But, given Your case, I would say that funds should rather go for runway expansion only, so that thew airport would have any economic future. As nowadays STOL-airports such as Yours face difficulties around the world, You should urgently fight to survive. Because such length of runway may cause that the airport will face very sad future...

Cheers,