If I understand correctly you are using the Arduino IDE/Monitor to communicate with your Arduino on COM3. You want to have Matlab connect to the Arduino.
Since RS-232 is a point to point methology, you can only have one program/device on each end unless you add a bunch of hijinks.
When you have the Arduino IDE/Monitor open it uses the com port and other programs are denied access.
I think you need to close the Arduino monitor program to release Com port 3 and then the Matlab program should be able to open the port.