I don't agree. MyISAM tables are easy to trash, and the table locking on update can bite you. There's no real disadvantage to using InnoDB other than having to learn to tune it a litte bit, and your data will be much safer.
MyISAM is like the ext2 filesystem. You crash and you end up spending a long time doing an fsck, where you have to verify the consistency by walking all the data structures. InnoDB is more like ext3, where you can make things consistent by replaying the changes in the journal. Doing repair on a large MyISAM table can take hours and hours.
The additional storage cost of InnoDB can be quite significant if you have a lot of data. We have about 4 billion rows in MyISAM, we simply wouldn't have space to do that with InnoDB.