The javadoc states that File.pathSeparatorChar is:
The system-dependent path-separator character. This field is initialized to contain the first chara
The PATH separator has been a semicolon for a very long time, presumably since the very first release of MS-DOS. (I'm assuming, as per Thorsten's answer, that Java simply defered to the Windows convention, presumably because Java programmers are likely to assume that they can use pathSeparatorChar
to parse the value of PATH rather than only to parse file lists produced by Java itself.)
The most obvious options for such a separator (by analogy with English) are the period, the comma, and the semicolon. The period would conflict with the 8.3 file name format. The choice of the semicolon over the comma may well have been arbitrary.
At any rate, semicolons were not legal characters in file names at that time, so there was no reason to prefer the comma. And, of course, since nowadays both commas and semicolons are legal, we wouldn't be any better off if they had. :-)