Motherboards can accept any SINGLE graphics card from either company. This issue is if (and only if) you're looking to combine multiple cards in SLI or Crossfire.
SLI and Crosfire are exclusive, proprietary technologies. SLI only works for Nvidia cards, Crossfire only works for ATI cards.
If you buy an SLI motherboard, you can only use the additional PCI-E slot(s) to combine identical Nvidia cards. You're free to use any single ATI card without any problems, though.
By the same token if you buy a Crossfire motherboard you can use any single card you want, from either company. But if you want to combine cards in Crossfire, they must be ATI cards from the same family/series.
ATI offers better value for your dollar. In order to get equivalent or better performance from Nvidia you need to spend more, that's just how their pricing is. For example the Radeon 4650 is slightly (about 5%, not 50%) better than Nvidia's 9500GT but costs the same. Meanwhile the Radeon 4670 is twice as fast for $10 more.
The Radeon 4850 and GTS 250 perform about identically, but the GTS 250 costs the same as the Radeon 4870, which is more powerful. Meanwhile the Radeon 4870 and GTX 260 are very close in performance (slight edge to the GTX 260), but again the 260 costs $35 more, the same price as a more-powerful Radeon 4890!
To beat the 4890, you need a GTX 275 which is more expensive, and so on... So going with Nvidia just means having to pay more. And currently ATI owns the high-end with their recent release of the 5000 series cards, which are the only DirectX 11 cards on the market. Nvidia won't have DX11 cards until next year when their 300 series is released.