I am very surprised with that. What phone are you using? I have an LG G5 that is pretty power hungy. if I plug it into the charger port in the arm rest, it doesn't register it as being plugged in. But I have found that on the USB on the front center console, it works to charging the phone. I have however found sometimes that you can plug in a phone and depending on the cable, it will decide that it doesn't want to charge. Are you using the original cable that came with the phone, or are you using a 3rd party cable? I would try a couple of different cables first as it might be a finiky cable that doesn't sync well with the power being provided by the port.
Are you using navigation and streaming? Lot of Android people have reported issues. No one with an iPhone. Might depend on the phone maker partially, but the USB amperage is definitely low. Some report using a 12 V adaptor works better, but then you no longer have Android Auto. Some have tried splitters without success so you can use a power adaptor and still run USB for data.
I agree, make sure you have a quality cable. I've used both charging places -- plugging into the USB with the other ports or the one in the bin. I have trouble keeping it at 100% all the time but I'm usually also listening to audio books and running a GPS logging program on it. Besides whatever else it thinks it should do... Hunting for wifi takes a lot of energy, so I try to remember to turn off wifi before anything but a very short trip.
Of course, if it's not showing charging, it's not charging. But even if it is, either the source or the cable may not be up to it. Get a good cable first. They may look the same, but they are not necessarily! If you charge with a cable in your house, try that one.
Ours also has the pad charger, but my phone gets pretty hot on that, so I don't use it much.
WiFi searching or sniffing takes very little energy (it is timed, not constant), and at least on iPhones, you get a warning that GPS will not be as good (probably meaning speed of location capture). It is likely that GPS will use more power without WiFi enabled. I suppose Android phones could be different, but they shouldn't be.
Anyway, I've had my phone on with WiFi enabled for hours while driving. No use of any kind, and no drop in battery percentage.