JNRH  My suggestion is: turn off layout view (View > Hide Layout), then resize the image down to a smaller size (double-click image to reveal resizing sheet). A large image combined with line spacing greater than 1 can cause the problem you describe to happen (it happens in Text Edit too). Alternatively, if you sandwich an image with two Returns, line spacing goes down to 1 and the image will show up. HTH   
(Version 2.1)

JNRH  I did some more research on this (I am Bean's developer). For me, under both Tiger and Leopard, when I open a file in Text Edit, select all text, open the Find panel, type 'a' under Find and 'b' under Replace, then press the Replace or the Replace & Find button, all the selected text is replaced with 'b.' So the whole selection is replaced with 'b.' Do you find this to be true? Let me know if we are talking about two different issues. Apple's Pages behaves similarly. So does OpenOffice Aqua. MS Word X reduces the selection size down to the first occurrence of the Find string, but doesn't replace it.

I will consider changing the behavior of the Find panel in Bean, because I agree with you that the Replace action should apply only to the text selection. But I am afraid of altering the standard way of doing things. Apparently the text selection typically takes precedence over the Find string when Replace is used, based on the behavior of the apps I described above, although that may simply be fore historical reasons.  
(Version 2.0.4b)

JNRH  The find panel and its behavior are supplied by OS X. The find panel behaves identically in Text Edit and all other apps that use the system-supplied find panel. Not that the behavior you describe is desirable, but it is standard OS X find panel behavior. Incidentally, Cmd-z will undo a find and replace, so data is not really 'lost' because the action is undoable.   
(Version 2.0.4b)