The issue you are running into is AutoReset. There are two different ways AutoReset can
be triggered.
One is using the DTR signal the other is using RTS.
If you have a board using DTR (which is most boards, including all the Official Arduino boards use), then
you are pretty much out of luck on disabling it in software as DTR is normally dropped by the operating system
driver when the serial port is opened by the application before the application gets control of the serial port.
If the board is using RTS instead, then this is not a problem and the application can open the serial port without
triggering auto-reset. The IDE and Avrdude have special code in them to trigger RTS so that is how
uploading still works when using RTS.
I prefer RTS over DTR as it allows uploading to use auto-reset but serial applications, terminal monitors
etc, can open the serial port for monitoring without triggering an auto reset.
Some Operating systems have options to configure/control the DTR behavior at serial port open/close,
but often it doesn't work correctly or at all.
Unix/linux/bsd has the stty hup options but not all of them fully support disabling DTR control.
Windows used to have an advanced serial port option
that allowed disabling the DTR signal processing on the serial port.
If the OS supports disabling DTR control on the serial open/close then
you can use it to allow opening the serial port without causing an auto-reset.
If not, you will need a hardware solution.
There are other 3rd party "arduino" boards out there like the Seeeduino that provide a switch/jumper to enable/disable
auto-reset. This is very nice as you can move the jumper/switch and disable auto-reset to prevent any software
from resetting the board no matter what the software tries to do or what signal is used (DTR vs RTS).
There are also some hardware kludges that involving adding a cap or resistor (depends on which board you have)
that can disable the auto-reset in hardware.
Google around for Arduino disable auto reset,
and you will find information on how to do it.
--- bill