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I got the Wrox.Beginning.JavaScript.3rd.Edition and wanted to start learning it from scratch, then my boss came along and said that why bother, learn jQuery. Can I understand jQuery and work with it although I am a newbie and have limited knowledge in ASP.net, vb.net, some C#, and basic HTML?!
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jQuery is javascript. I think you're on the right path. Learn javascript well and you'll be able to make better use of jQuery.
Libraries will alwas contain nonessential complexity, but they can save some headaches if they're not too bloated or already present on the end users' systems. Best use would be to learn javascript while using jquery, and then slowly remove the crutch of using jquery. While it's powerful, it does add significant overhead, nonessential complexity, and potential opportunities for abuse, just like flash. There are no silver bullets.
jQuery removes the need for many bad Javascript habits. However, you will frequently need to know more than just jQuery to get non-trivial work done.
You'll need to learn both, but try to pick up habits based on jQuery.
I would say the statement is akin to you reading a C#/VB.Net book and having your boss say "Don't bother, just learn ASP.Net". You really don't get much from the latter without the former.
Maybe your boss is trying to save you some time learning the basics of Javascript and start you off learning jQuery right away but I think this would be a bad idea.
Understanding the basics of javascript is key to using jQuery successfully. jQuery provides shortcuts and solutions to problems (cross browser problems etc) but it is not a language unto it's self.
My advice, learn javascript, learn about handling events in different browsers, inserting in to the DOM and then start using jQuery. You will appreciate it a lot more and be a better coder for it.
JQuery provides a good layer of abstraction for interacting with DOM elements. You can do a lot of interesting things with it quickly and easily. But there are probably many things that JQuery won't do for you. You'll need to use regular JavaScript for that.