Did you try to convert your special characters before writing them to your PDF?
yourHTMLString.replaceAll(oldChar, newChar);
ć = ć
ř = ř
ě = ě
If you need more special characters, visit this link.
EDIT: Then try this out, it worked for me:
BaseFont basefont = BaseFont.createFont("C:/Windows/Fonts/ARIAL.TTF", BaseFont.IDENTITY_H, BaseFont.EMBEDDED);
Font font = new Font(basefont, 12);
document.add(new Paragraph("čřě", font));