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Eric Wedge has nothing against walking, despite his public stance on patience.  His first year as manager of the Indians in 2003, the team had teh 22nd ranked offense with the 26th ranked walk rate.  Over the next 6 years as the manager of the Indians, he resided over a team with the 5th best offense and the 9th best walk rate.  The only point I am trying to make is that we was not an impediment to his Indians teams taking a walk.
So why the present stance in Seattle?  DaddyO has arrived at a similar conclusion to me, though I suspect the reasons for sitting Cust are more than just the absence of home runs.  After all, he is sitting to the benefit of Adam Kennedy and it is not like Adam is a huge home run threat.  I think that Jack's only skill is trying to walk.  He has lost the ability to punish a mistake or a centered fastball, so his contribution to the team in the present is minimal and zero to the future.
Let's say you figure Jack Cust has a 85% chance of out hitting Greg Halman, but the what you get for it is mediocrity at best in the present and nothing in the future.  Who do you play?
Last point I'd like to make is that if one takes a historical view of hitting in the bigs, the number of singles hitters with high walk rates is very low.  For every one Dave Madagan, you get ten Willie McGee's.  For every one Wade Boggs, you get ten Rod Carew's.  I think Eric Wedge saw a bunch of punchless wonders trying to work deep counts and letting good pitches go by when he knew the pitcher had no reason to fear the batter.  If the worst you have to fear from a hitter is a ground ball single (Jack Wilson, Brendan Ryan, Ichiro, Gutierrez, etc), you challenge them early in the count and then put them away.  If by chance you fall behind, you can still challenge them later in the count.  What do you have to loose?
Of the M's that get regular playing time, Justin Smoak is the only player with a positive performance against fastballs according to pitch values at fangraphs.  If you cannot manage hitting fastballs in the bigs, you will not succeed.  As an aside, this is also why I am concerned about Ichiro.  Disregarding 2005 when he changed his approach to appease Mike Hargrove (more power, more walks, and less effectiveness for those that want to make Ichiro a home run hitter), Ichiro had positive results for from 2002 to 2009.  He was slightly negative last year, and is doing much worse this year.  The results indicate he's lost enough bat speed to struggle with fastballs which is the beginning of the end.