I find this bit very unnerving. Security checks in Jakarta are a part of daily life. You will be subjected to a check at every hotel and major shopping complex that you visit. The security checks came about after the Bali bombings and they've been here ever since.
For example, each time our driver enters the hotel car park, we are subjected to a check by the guards posted there. The guards will take a look inside our car and open the boot (trunk?) to check for any suspicious packages. Some places also have a guard using a mirror to check the bottom of your car. The checks are usually brief and they'll wave us on with a smile and an apology for disturbing us. Indonesians are very friendly and polite, they're much friendlier than we Malaysians are.
At the hotel entrance, there will be a metal detector and a guard waiting for you. There is usually a table next to the detector, so place your handbag there for them to inspect while you walk through the detector. You collect your bag after you have passed through.
I am not sure what these checks accomplish. Some of the guards don't appear to be doing a thorough job at checking anyway and all it does is to make me nervous. I keep thinking that a bomber is going to appear at any moment!