The Luddites amonst us (none on this board, thankfully) are so terrified at the mere mention of Plutonium that putting RTGs on a spacecraft really drives up the cost, largely due to all of the environmental impact studies and the like. Programs like MER have such tight budget constraints that using RTGs just might not have been possible, no matter how desireable or how much sense they make. Pity.

There may also be a weigh constraint. RTGs use the heat from Pu 238 decay (87 year half life) and thermocouples to generate electricity. A thermocouple is only about 2-5% efficient at converting heat into electricity, so an RTG capable of producing the 300+ watts needed by the rovers might've been too heavy compared to solar panels and batteries.