Connector Selection Criteria
This is a very broad question, as the reasons are as numerous as the number of connectors out there.

Here are some of the most important points to consider when choosing a connector system. The last point may be the reason for your friends  decision for RJ45.


Electric properties


High voltage
HV may require connectors with special insulation. It's also possible that the user should be protected from touching the contacts.
On the other side, tiny voltages may need some shielding against interference, not only for the cable, but also for the connector.
Maximum Current
High currents need large contacts and sometimes, you also need a very low contact resistance.
Note also that the contacts of the common SubD connector can be made of thin sheets of metal capable of some 100mA, but can also be made of massive, machined metal rated for 2A.
High Frequency
Connectors must not only match the shape of the cables, but also often its electrical characteristics like shielding and impedance.
Hot-plugging / plug detection
Have a look at USB or SATA cables. Some contacts are longer than others, so they will connect as first / disconnect as last. Plugs for audio jacks often contain a switch to detect a plugged in jack.

Mechanic properties


Number of contacts
Size
Tiny devices need tiny connectors. I worked on a project where we were happy to find an inter-PCB connector of 0.8mm height.
Type of assembly
Is the connector soldered / crimed / screwed / connected to an other connector?
Contact durability
There are connectors specified for 10 plug/pull cycles only, which are used inside devices and usually plugged only once, during production. For an audio jack, you definitely want more.
Durability
Sometimes, you need more heavy-duty like connectors. Some connectors need to be water tight, others should not disconnect e.g. due to vibrations.
Uniqueness
If you design a device with ten different cables being connected to, use ten different connectors, if possible. This makes it impossible to connect the device the wrong way. USB uses different connectors on both sides, because one side is connected to a host (PC), and the other to a client (Device). However, with USB-on-the-go this principle has been weakened. 
Choice of material
The connector may have to withstand high / low temperatures, chemicals, may not contain materials becoming toxic when burning, and so on. I worked on projects with high magnetic fields, where connectors had to be non-magnetic (iron/nickel-free).

Economic reasons


Easier / faster assembly
The price for a custom connector may be worth a faster assembly of your product, if the quantity is high enough.
Customers loyalty
Dell uses a special connector for their laptop power cords, and there are not many third-party manufacturers of power supplies with that connectors. So, people buy Dell's genuine devices. (though this situation has relaxed somewhat). There is that cool company producing computers and mobiles. They make heavy use of custom connectors, so consumers have to buy at least a bunch of adaptors to use any kind of peripherals... 
Synergy effects
Sometimes, there already is a well established mass marked of a connector / cable system, making it exceptionally cheap.
You mentioned RJ45. You can get connectors and cables of any length nearly for free, and the electric properties are quite good. Current is limited, but you get a handy, thin cable with four twisted pairs, may be shielded with a quite good impedance. Remember, computers transfer up to 1GBit/s through that cables. So yes, why not use it for other digital communication stuff?
Another example: In an experiment, we needed a bandwidth of several Gigabit/s. They used HDMI, because cables, connectors and transmitter/receiver modules were already available. Don't ask for the details, but HDMI, made for video transmission, had some benefits, so we use it to read out detectors in high energy physics.