I'm pretty sure glass is transperent, it's hard to code as well, I hear raining outside and take a glance off my window for the beautiful weather, but all I see the the rain hitting ground particles. :l
Hope this gets fixed soon.
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Vote to get the bug more priority and giving it attention so it is fixed.

This bug effects Minecraft Pocket Edition also.
This is partially fixed in 1.2.13.5 - there are some remaining situations where rain does not render through glass that can't be fixed, however.

Rain cannot be seen through east and south windows but visible through north and west. Update 15.1 today.
This bug has been reported to our internal bug tracker for further testing and a fix. It is scheduled to be fixed in one of the future updates (no specific date can be provided).