How can I use a 12VDC bilge pump with an Intermatic timer for pond circulation?
A couple things could be going on, as @bib and @BMitch allude:


Your transformer could be putting out AC 12V instead of DC 12V. (Sometimes these are labeled VAC and VDC, respectively.)
Your transformer may not be able to supply enough current to power the pump. The pump and transformer should both have their current listed (in the case of the transformer it will be a max current). If the pump is trying to draw more than the transformer can supply, both will be unhappy.
Your pump could be sensitive to polarity and you've got the two wires crossed. I think most DC motors should work forwards and backwards, but of course the pump will only function properly one direction.
If the transformer is cheap it may be putting out "noisy" DC power which the pump isn't liking. A car battery puts out pure DC power but the transformer needs to rectify and filter your household AC power, and some transformers are better than others.