This is an old question, but it's still relevant and one of the top result when searching for a solution and, yet, the main solution is not yet in any so here you go...
The "Root Transform" check boxes in any animation are used to apply the movement of the root object to the the in-game character transform. If it's checked ON, it allows the root object translation (movements) to be copied onto the object's transform in an additive while if it's OFF, the animation motion will be added to the object's transform, but will also include the part where it loop back (for example, with a walk animation with Root Motion, it will looks like the character is rubber-banding back to its start position once the animation is done.)
"Root Transform" is useful in cases, for example, where you want to customize the movement of the character based on its animation without coding all the variances in speed and direction. (For example, if you want the character to step forward during an attack or if you want a character to move at the representative speed of its steps and not just moon-walking.)
Outside of Unity, there are a lot of ways of handling the issue (some are easy and some are time-consuming), but Unity itself has a built-in way that is relatively straight forward.
To do it directly in Unity (for example, with animation you got from some assets purchased from the Asset Store), go to the FBX file, in the Unity Project menu, that contains the animation(s) you need. (Note: The animations HAS to be applied to the "Animation" tab of the FBX first.) Open the FBX file content by clicking on the arrow right or left to it (depending on the type of display). You should see each animation set in the FBX (the icon is a cyan triangle with some white or black lines on its left) Select all the animation, copy (CTRL+C) and paste (CTRL+V) them outside of the FBX file. Unity will generate animation files based on the animation settings set in the FBX.
Those animation files that get copied and pasted can be edited in the "Animation" menu in Unity. You can remove the root motion from those file by looking up, in the "Animation" menu for the Animator.Root.T line of keyframe.
Each animated bones in the animation will have 2 lines of keys. One is ending with "T" which is the Transform (movement) and one is the "Q" which is the Quaternion (rotation). You might think of just deleting them both, but remember that it will remove ALL position and rotation references. If you got a skill that turn the character 360 degrees for an attack, that turn will most likely disappears if you remove the "Root Q" keys. At the same time, if you just remove the "Root T" keys, the character might end up being offset from the proper position.
So, the trick is to uncheck the Root Transform Rotation and Position(Y) and (XZ), which can be done in the animation file you copied and pasted, go to the "Root Q" and "Root T" line of animation keys in the Animation menu. If you don't need any rotation (like for a walking/run that is straight forward), you can deleted the "Root Q" line of keys. (you can delete a whole line just by clicking on the white dot right of the "Root Q" and select "Remove Property".)
For the "Root T", line, it needs a bit more subtleties: You got to open the drop-down (arrow right of the animation key line name) which will reveal the 3D movements axes (X,Y,Z) of the animation root. You can delete the property (as previously mentioned) for the X and Z unless you need them (for specific animations) and if you don't need any of the Y keys, you can just delete all keys of that line (do NOT delete the property), except for the first key. This can easily be done by selecting the 2nd key, then while holding shift, click on the last key and then press Delete. If There's only 1 key (the first one), the animation will not have root motion, but it will still have its proper "default" position.
If you delete the whole line of keys on "Root T.y", there's a chance your character will be positioned with its pelvis position as its "origin" instead of its root position, resulting with your character being quite lower than anticipated visually.