The difference is usually in the DPI (dots per inch) configuration in the screen resolution. The resolution of a screen is not enough to determine the mapping to an absolute size for a font (72 points/inch). The additional information, DPI, provides the missing piece.
Depending on your distribution, video card driver and desktop environment, the DPI setting can be changed in several places. In current Gnome for example, you can set it by going to menu System->Preferences->Fonts, click on the Details button, and the DPI setting will be available at the top of the dialog.
Keep in mind that your Windows setting may be wrong too!
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