This refers to version 0.9.0 RC4.
One should avoid to print the document to a PDF file via the CUPS PDF pseudo-printer (the one that outputs to ~/PDF by default). This creates a file ~/PDF/Java-Printing.pdf, but it uses Adobe Type 3 fonts (bitmap fonts), which reduces the effective print resolution and optical quality, and makes the PDF about 10 times larger than necessary, by embedding the bitmap fonts.
One should also avoid to use the “File -> Export -> As PDF …” feature of FreeMind. This creates also PDFs that are approx. 10 times larger than necessary, but this time because text is converted to paths. This also makes it impossible to select and copy text in the PDF. And finally, the page size cannot be set when exporting (you probably want e.g. DIN A4), which however can be corrected by importing the PDF into Inkscape and exporting again to PDF; which however does not work for embedded PNGs with transparency, as they get a black background. And really, finally, this kind of export has problems with colors: they appear more intense in the PDF in Adobe Reader.
The best way is to print from FreeMind to any printer and select “redirect to file”. This will create a small PostScript file, which you can convert to PDF using the ps2pdf command. This creates a nice PDF: minimum size, embedded Type 1 vector fonts, selectable text, no problems with transparent embedded PNGs.
Using this solution has the difficulty of getting the output correctly positioned and scaled on the page. The best way is to set the page margins of the printer you use to minimum amounts (care: this is not reflected in the page preview!), and use the “File -> Page settings -> Scale to Page Size” setting (this is reflected in the page preview, so check there). And then to modify your mindmap so that its aspect ratio fits well to your page size, without wasting much space; you can check that in the page preview. And finally, check the effective (scaled) font sizes by opening the PDF document in Adobe Reader at 100% zoom and see if you can read it.