OpenGL versions generally add new functionalities to previous versions, so I'd say that learning OpenGL 4.1 is in fact learning OpenGL 3.0, as the base is the same, especially if you're beginning 3d programming.
OpenGL ES 2.0 is a kind of subset of OpenGL 3.x.
With these 'facts' in mind, I'd say that learning OpenGL 3+ or OpenGL ES 2+ is about the same, with differences in details.
Note that depending on your desktop platform (OS, graphics card), you may not have access to an OpenGL 3 implementation.
An implementation of OpenGL ES 2 on desktop may also not be available.
Shezan Baig suggestion to startin with WebGL may help you with this, as it delegates the OpenGL init. problem to the browser - some even implement WebGL over DirectX to improve its availability.
My suggestion is that, while you learn, you focus on 3d principles, algorithms, and maths. These are the hardest to get right. Implementation 'details' don't vary much with OpenGL (ES or not) or DirectX, or whatever.
More precisely, I'd suggest that you start in the programming language you're most familiar with. I'd go with OpenGL 1.x/2.x in this language : these 'old' versions of GL contain lot of helper functions (glBegin/glVertex/glEnd ; glMultMatrix ; etc.) that are 'deprecated' in 3.x+. Using these, you'll be more 'productive' for testing algorithms.
There are many things in 3d programming, you can find reference books that have become freely available, and select what information is interesting for your use-case.