The downsides to an HTPC blu-ray player are as follows:
#1 3rd party software is required to play BD discs. PowerDVD, Total Media Theatre, etc. is needed and add to the overall cost $70-100. Most of the bundled software you get with a BD drive is crippled in some way, like only 2 channel audio.
#2 Until 2010, it is rather expensive to get HD audio to bitstream over HDMI with an HTPC. Right now you either need a high-end video card (HD5850) or a $130 sound card (Auzentech or Asus Xonar). Standard DD or DTS or passing LPCM is not a problem though. Standalones easily bitstream HD audio through HDMI. Cheaper HD5xxx cards are expected in 2010 that will make this point moot however.
#3 The total cost of a complete HTPC system will be more than just a standalone. However, it can do a lot more too.
#4 With a standalone you just plug it in and turn it on. An HTPC requires setup... AND maintenance.
The upsides to an HTPC are as follows:
#1 You can rip BD discs and store media locally.
#2 It's upgradeable so you can keep up with technology as it progresses.
#3 HTPC's can take advantage of all online media services like Netflix, Hulu, and whatever may come in the future. Some standalones have streaming available from services like Netflix, but what you got is all you get.
#4 HTPC's can do A LOT more than play blu-rays. Period.
So basically, it is not worth it to build an HTPC if all you want to do is watch blu-rays. Standalones will win hands down. If you are technically inclined, don't mind tweaking, and/or get satisfaction from creating a custom AV piece of art that can grow with your media needs then an HTPC is more suited.