Are you not "allowed" to assign a transaction to a main category?

Parent categories represent a challenge for Quicken and Quicken deals with it inconsistently.
And solution might be to use another subcategory, I lot of people say not to put anything into a parent category.

A parent category can be four things at the same time.

1. Holder of subcategories.
2. A "place" to select you want to report on everything under it.
3. A "place" to select only the parent category.
4. Category for transactions.

First let's look at the oldest of them, reports and how they work.
There isn't anything called Everything Else.  Everything Else is the concept that even though you didn't include certain categories, you might be blind sighted by them if they don't show them to you.

Also, the budget is grouped by "category groups".  There are a few built in ones like "Personal Expenses", and you can create custom ones.  These act like "super parent categories".  And I should point out that are two kinds of Everything Else.  One is attached to the category group and another to the parent category.
For the category group:


For the parent category:


Reports show you exactly which categories you have selected, and only them.
Its selection box looks like this.


If I select only Utilities that is exactly what I'm going to get, I'm not going to get Backup, Cable TV, ...

Budget Graph View.
The category group Everything Else is going to show up if you have not selected all the categories.  It has been requested many times that the user should be able to control showing it, but just like the "More Accounts" the Quicken Windows management/developers have refused to do that (from what I understand they can do it on Quicken Mac).
Its selection box looks like this:

I need to point out "Other" and how selecting just Utilities works in the budget.  If you select just Utilities unlike in the reports the budget takes this to mean that you want to include the parent category and all the subcategories.  "Other" might look like a subcategory but it isn't.  In the budget it means the parent category.  So, if all I selected above is Other than it would show mean only the Utilities category.

What makes the parent category Everything Else show up is selecting the parent category and at least one subcategory, but not all of them like this:

This is weird combination if you think about it.  If I select only Home it means report on Home and everything below it, but as soon as I select a subcategory it takes that to mean that you don't want to show the other subcategories separated, but you do want to see their total "Everything Else".

Now for the budget Annual View.
The Annual View doesn't have an Everything Else for the category groups, so it is inconsistent with Graph View.  The rest is the same.

@Chris_QPW there once was a time when the parent Category was only used for and selected when: You wanted to select ALL the sub categories, and actually that had it's merit and I personally liked it better!