The fact that you felt uncomfortable is valid in itself.
Er, no it isn't. Lots of medical procedures, examinations and investigations make you feel uncomfortable.
Some people talk about an old fashioned type of vaginal examination. It is not old fashioned and is still taught at medical schools. It's called a bimanual exam, bimanual because both hands are used. Basically the clinician inserts two gloved and lubricated fingers inside the vagina and the other hand on the lower abdomen. By palpating the cervix and pressing on the abdomen the top of the uterus can be felt from the outside (the fundus). This gives information about its position, size and if it causes pain, health. By moving the fingers inside the vagina towards the left and right aspects of the vaginal vault (ie the top of the vagina either side of the cervix) and pressing upwards the adnexae can be examined from the outside. These are the areas internally either side of the uterus where the ovaries and fallopian tubes lie. Pressing down with the outside hand allows masses to be felt in these areas and can localise them with some accuracy.
A speculum is used to visualise the cervix and is another routine investigation. If someone has bleeding after sex for example then this might indicate some (usually completely normal) change to the skin covering the cervix and this can be seen on speculum exam.
It's not pleasant having either of these procedures done and it feels odd having a stranger's fingers inside your vagina. It's also uncomfortable learning to do these procedures at the beginning because they relate to examining sexual organs. And if they are done thoroughly it takes a few minutes to complete a full bimanual and speculum exam.
I had surgery a few years ago for something called a rectocele. This is where the rectum herniates into the vagina causing a bulge inside the vagina. It can cause constipation and discomfort. It's nearly always related to childbirth injury (it was in my case) and is based on the normal fascia in between the two cavites being weakened or damaged. It can also be associated with uterine prolapse (where the uterus is less well held up and drops down into the upper vagina).
Anyway, long story but to check for a prolapse a good gynaecologist cannot just examine for it with the patient lying down. So I had a thorough bimanual exam lying down and then had to stand up to be examined internally (simply because gravity causes things to drop down, so unless you allow gravity to work you cannot tell if there is prolapse). I undressed behind the curtain and I had to stand undressed from the waist down while a male, very smartly dressed gynaecologist stood in front of me and inserted two gloved fingers into my vagina to feel for any degree of prolapse. Thankfully there was none. I also had to squeeze his fingers so he could check the strength of the muscles of my pelvic floor.
I admit at the time it was impossible to completely dissociate it from sexual things. Why? Because I had never had a man put his fingers into my vagina when I was standing up unless I was having sexual contact with him. And it felt pleasurable in some ways, not because I saw the gynaecologist in a sexual way or because he was in any way unprofessional but because it was a pleasant sensation physically despite the context.
But it was all normal and appropriate; actually he was doing his job well because if he had not done a thorough examination - including examining me standing - he might not then have made such a successful job of my later surgery.
There is more sensitivity perhaps (reluctance?) to perform intimate examinations than there was once. This can be appropriate. If a woman comes for her six week check after having a baby she is offered a pelvic exam if she has any concerns or wants her stitches checked etc, but it is not insisted upon and if she doesn't feel the need for it then it isn't necessary.
But simple physical examinations can provide lots of information for doctors and nurses. They can reveal things like fibroids, ovarian tumours and if they cause some pain this can also be indicative of underlying pathology.
It's very important to be aware that there are, very rarely, cases where clinicians sexually assault patients and to be vigilant to this happening.
But it's also important to understand why these exams are done and to accept that they involve actions (like putting fingers into a vagina) that we all associate with a sexual context. That doesn't in itself make them inappropriate or sexual in themselves, though it does feel psychologically uncomfortable for the patient (usually not the doctor or nurse, unless they are very very inexperienced).
I hope this is helpful.