<br> can be abused as one of those presentation tags, not as offensive as <font> but still a little. The modern thinking is that on the client-side (the browser) you have the three layers:
content - HTML/XHTML
presentation - CSS
Mixing the three layers is a bad practice, for example defining colors inside the HTML. The HTML should be only the content, like XML with no hints as to how it will be displayed. The content should be semantic, each tag describing the content, like <ul> and <ol> for lists and so on.
If you need a new line, that's more often a new paragraph, so you should probably use a <p> tag. Now sometimes you need a new line that is not a paragraph, like when in Word you hit SHIFT+ENTER. That's fine, but having two <br>s one after the other smell like a paragraph. If you find yourself using several <br>s in sequence, that's a sign that maybe you should use CSS to achieve the desired presentation.
I don't think there's anything wrong with the <br> tag per se, but it shouldn't be abused.
I see that even in HTML 5 it won't be deprecated, because it has its semantic meaning - a line break.